Add function to import seafloor crustal age dataset (#1471)

New function to download the Earth seafloor age datasets
at various resolutions. This is the `@earth_age` grids on the
GMT remote data server.

* add earth_age.py
* Add test_datasets_earth_age.py
* add seafloor age datasets to helpers/testing.py
* add load_earth_age to index.rst
* add 05m grid tile for caching

Co-authored-by: Wei Ji <[email protected]>

Author: willschlitzer

doc/api/index.rst

@@ -170,6 +170,7 @@ and store them in the GMT cache folder.
 .. autosummary::
     :toctree: generated
 
+    datasets.load_earth_age
     datasets.load_earth_relief
     datasets.load_fractures_compilation
     datasets.load_hotspots

pygmt/datasets/__init__.py

@@ -2,6 +2,7 @@
 #
 # Load sample data included with GMT (downloaded from the GMT cache server).
 
+from pygmt.datasets.earth_age import load_earth_age
 from pygmt.datasets.earth_relief import load_earth_relief
 from pygmt.datasets.samples import (
     load_fractures_compilation,

pygmt/datasets/earth_age.py

@@ -0,0 +1,113 @@
+"""
+Function to download the Earth seafloor age datasets from the GMT data server,
+and load as :class:`xarray.DataArray`.
+
+The grids are available in various resolutions.
+"""
+from pygmt.exceptions import GMTInvalidInput
+from pygmt.helpers import kwargs_to_strings
+from pygmt.io import load_dataarray
+from pygmt.src import grdcut, which
+
+
+@kwargs_to_strings(region="sequence")
+def load_earth_age(resolution="01d", region=None, registration=None):
+    r"""
+    Load Earth seafloor crustal ages in various resolutions.
+
+    The grids are downloaded to a user data directory
+    (usually ``~/.gmt/server/earth/earth_age/``) the first time you invoke
+    this function. Afterwards, it will load the grid from the data directory.
+    So you'll need an internet connection the first time around.
+
+    These grids can also be accessed by passing in the file name
+    **@earth_age**\_\ *res*\[_\ *reg*] to any grid plotting/processing
+    function. *res* is the grid resolution (see below), and *reg* is grid
+    registration type (**p** for pixel registration or **g** for gridline
+    registration).
+
+    Refer to
+    :gmt-docs:`datasets/remote-data.html#global-earth-seafloor-crustal-age-grids`
+    for more details.
+
+    Parameters
+    ----------
+    resolution : str
+        The grid resolution. The suffix ``d`` and ``m`` stand for
+        arc-degree, arc-minute and arc-second. It can be ``'01d'``, ``'30m'``,
+        ``'20m'``, ``'15m'``, ``'10m'``, ``'06m'``, ``'05m'``, ``'04m'``,
+        ``'03m'``, ``'02m'``, or ``'01m'``.
+
+    region : str or list
+        The subregion of the grid to load, in the forms of a list
+        [*xmin*, *xmax*, *ymin*, *ymax*] or a string *xmin/xmax/ymin/ymax*.
+        Required for grids with resolutions higher than 5
+        arc-minute (i.e., ``05m``).
+
+    registration : str
+        Grid registration type. Either ``pixel`` for pixel registration or
+        ``gridline`` for gridline registration. Default is ``None``, where
+        a pixel-registered grid is returned unless only the
+        gridline-registered grid is available.
+
+    Returns
+    -------
+    grid : :class:`xarray.DataArray`
+        The Earth seafloor crustal age grid. Coordinates are latitude and
+        longitude in degrees. Age is in millions of years (Myr).
+
+    Notes
+    -----
+    The :class:`xarray.DataArray` grid doesn't support slice operation, for
+    Earth seafloor crustal age with resolutions of 5 arc-minutes or higher,
+    which are stored as smaller tiles.
+    """
+
+    # earth seafloor crust age data stored as single grids for low resolutions
+    non_tiled_resolutions = ["01d", "30m", "20m", "15m", "10m", "06m"]
+    # earth seafloor crust age data stored as tiles for high resolutions
+    tiled_resolutions = ["05m", "04m", "03m", "02m", "01m"]
+
+    if registration in ("pixel", "gridline", None):
+        # If None, let GMT decide on Pixel/Gridline type
+        reg = f"_{registration[0]}" if registration else ""
+    else:
+        raise GMTInvalidInput(
+            f"Invalid grid registration: '{registration}', should be either "
+            "'pixel', 'gridline' or None. Default is None, where a "
+            "pixel-registered grid is returned unless only the "
+            "gridline-registered grid is available."
+        )
+
+    if resolution not in non_tiled_resolutions + tiled_resolutions:
+        raise GMTInvalidInput(f"Invalid Earth relief resolution '{resolution}'.")
+
+    # Choose earth relief data prefix
+    earth_age_prefix = "earth_age_"
+
+    # different ways to load tiled and non-tiled earth relief data
+    # Known issue: tiled grids don't support slice operation
+    # See https://github.com/GenericMappingTools/pygmt/issues/524
+    if region is None:
+        if resolution not in non_tiled_resolutions:
+            raise GMTInvalidInput(
+                f"'region' is required for Earth age resolution '{resolution}'."
+            )
+        fname = which(f"@earth_age_{resolution}{reg}", download="a")
+        grid = load_dataarray(fname, engine="netcdf4")
+    else:
+        grid = grdcut(f"@{earth_age_prefix}{resolution}{reg}", region=region)
+
+    # Add some metadata to the grid
+    grid.name = "seafloor_age"
+    grid.attrs["long_name"] = "age of seafloor crust"
+    grid.attrs["units"] = "Myr"
+    grid.attrs["vertical_datum"] = "EMG96"
+    grid.attrs["horizontal_datum"] = "WGS84"
+    # Remove the actual range because it gets outdated when indexing the grid,
+    # which causes problems when exporting it to netCDF for usage on the
+    # command-line.
+    grid.attrs.pop("actual_range")
+    for coord in grid.coords:
+        grid[coord].attrs.pop("actual_range")
+    return grid

pygmt/helpers/testing.py

@@ -165,6 +165,9 @@ def download_test_data():
         "@N35E135.earth_relief_03s_g.nc",
         "@N37W120.earth_relief_03s_g.nc",
         "@N00W090.earth_relief_03m_p.nc",
+        # Earth seafloor age grids
+        "@earth_age_01d_g",
+        "S90W180.earth_age_05m_g.nc"  # Specific grid for 05m test
         # Other cache files
         "@EGM96_to_36.txt",
         "@fractures_06.txt",

pygmt/tests/test_datasets_earth_age.py

@@ -0,0 +1,78 @@
+"""
+Test basic functionality for loading Earth seafloor crust age datasets.
+"""
+import numpy as np
+import numpy.testing as npt
+import pytest
+from pygmt.datasets import load_earth_age
+from pygmt.exceptions import GMTInvalidInput
+
+
+def test_earth_age_fails():
+    """
+    Make sure earth_age fails for invalid resolutions.
+    """
+    resolutions = "1m 1d bla 60d 001m 03".split()
+    resolutions.append(60)
+    for resolution in resolutions:
+        with pytest.raises(GMTInvalidInput):
+            load_earth_age(resolution=resolution)
+
+
+def test_earth_age_incorrect_registration():
+    """
+    Test loading earth_age with incorrect registration type.
+    """
+    with pytest.raises(GMTInvalidInput):
+        load_earth_age(registration="improper_type")
+
+
+def test_earth_age_01d():
+    """
+    Test some properties of the earth age 01d data.
+    """
+    data = load_earth_age(resolution="01d", registration="gridline")
+    assert data.shape == (181, 361)
+    npt.assert_allclose(data.lat, np.arange(-90, 91, 1))
+    npt.assert_allclose(data.lon, np.arange(-180, 181, 1))
+    npt.assert_allclose(data.min(), 0.167381, rtol=1e-5)
+    npt.assert_allclose(data.max(), 338.0274, rtol=1e-5)
+
+
+def test_earth_age_01d_with_region():
+    """
+    Test loading low-resolution earth age with 'region'.
+    """
+    data = load_earth_age(
+        resolution="01d", region=[-10, 10, -5, 5], registration="gridline"
+    )
+    assert data.shape == (11, 21)
+    npt.assert_allclose(data.lat, np.arange(-5, 6, 1))
+    npt.assert_allclose(data.lon, np.arange(-10, 11, 1))
+    npt.assert_allclose(data.min(), 11.293945)
+    npt.assert_allclose(data.max(), 125.1189)
+
+
+def test_earth_age_05m_with_region():
+    """
+    Test loading a subregion of high-resolution earth age.
+    """
+    data = load_earth_age(
+        resolution="05m", region=[-50, -40, 20, 30], registration="gridline"
+    )
+    assert data.coords["lat"].data.min() == 20.0
+    assert data.coords["lat"].data.max() == 30.0
+    assert data.coords["lon"].data.min() == -50.0
+    assert data.coords["lon"].data.max() == -40.0
+    npt.assert_allclose(data.data.min(), 0.040000916)
+    npt.assert_allclose(data.data.max(), 46.530003)
+    assert data.sizes["lat"] == 121
+    assert data.sizes["lon"] == 121
+
+
+def test_earth_age_05m_without_region():
+    """
+    Test loading high-resolution earth age without passing 'region'.
+    """
+    with pytest.raises(GMTInvalidInput):
+        load_earth_age("05m")