roms-tools 2.7.0__py3-none-any.whl → 3.1.0__py3-none-any.whl

roms_tools/tests/test_setup/test_grid.py

@@ -1,17 +1,29 @@
-import pytest
+import copy
+import importlib.metadata
 import logging
+import textwrap
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+import numpy as np
+import numpy.testing as npt
+import pytest
 import xarray as xr
+from scipy.ndimage import label
+
+from conftest import calculate_file_hash
 from roms_tools import Grid
-import importlib.metadata
-import textwrap
+from roms_tools.constants import (
+    MAXIMUM_GRID_SIZE,
+    UPPER_BOUND_THETA_B,
+    UPPER_BOUND_THETA_S,
+)
 from roms_tools.download import download_test_data
-from conftest import calculate_file_hash
-from pathlib import Path
+from roms_tools.setup.topography import _compute_rfactor
 
 
 @pytest.fixture()
 def counter_clockwise_rotated_grid():
-
     grid = Grid(
         nx=1, ny=1, size_x=100, size_y=100, center_lon=-20, center_lat=0, rot=20
     )
@@ -21,7 +33,6 @@ def counter_clockwise_rotated_grid():
 
 @pytest.fixture()
 def clockwise_rotated_grid():
-
     grid = Grid(
         nx=1, ny=1, size_x=100, size_y=100, center_lon=-20, center_lat=0, rot=-20
     )
@@ -29,8 +40,83 @@ def clockwise_rotated_grid():
     return grid
 
 
-def test_grid_creation(grid):
+@pytest.fixture()
+def grid_that_straddles_dateline_with_shifted_global_etopo_data():
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=1000,
+        size_y=1000,
+        center_lon=0,
+        center_lat=0,
+        rot=20,
+        topography_source={
+            "name": "ETOPO5",
+            "path": download_test_data("etopo5_coarsened_and_shifted.nc"),
+        },
+    )
+
+    return grid
+
 
+@pytest.fixture()
+def grid_that_straddles_dateline_with_global_srtm15_data():
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=1000,
+        size_y=1000,
+        center_lon=0,
+        center_lat=0,
+        rot=20,
+        topography_source={
+            "name": "SRTM15",
+            "path": download_test_data("srtm15_coarsened.nc"),
+        },
+    )
+
+    return grid
+
+
+@pytest.fixture()
+def grid_that_straddles_180_degree_meridian_with_shifted_global_etopo_data():
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=1000,
+        size_y=1000,
+        center_lon=180,
+        center_lat=0,
+        rot=20,
+        topography_source={
+            "name": "ETOPO5",
+            "path": download_test_data("etopo5_coarsened_and_shifted.nc"),
+        },
+    )
+
+    return grid
+
+
+@pytest.fixture()
+def grid_that_straddles_180_degree_meridian_with_global_srtm15_data():
+    grid = Grid(
+        nx=5,
+        ny=5,
+        size_x=1000,
+        size_y=1000,
+        center_lon=180,
+        center_lat=0,
+        rot=20,
+        topography_source={
+            "name": "SRTM15",
+            "path": download_test_data("srtm15_coarsened.nc"),
+        },
+    )
+
+    return grid
+
+
+def test_grid_creation(grid):
     assert grid.nx == 1
     assert grid.ny == 1
     assert grid.size_x == 100
@@ -75,13 +161,35 @@ def test_coords_relation(grid_fixture, request):
     assert_smaller_equal_than_with_tolerance(grid.ds.lon_v.max(), grid.ds.lon_rho.max())
 
 
-def test_plot_save_methods(tmp_path):
+@pytest.mark.parametrize(
+    "grid_fixture",
+    [
+        "grid_that_straddles_dateline",
+        "grid_that_straddles_180_degree_meridian",
+        "grid_that_straddles_dateline_with_shifted_global_etopo_data",
+        "grid_that_straddles_180_degree_meridian_with_shifted_global_etopo_data",
+        "grid_that_straddles_dateline_with_global_srtm15_data",
+        "grid_that_straddles_180_degree_meridian_with_global_srtm15_data",
+    ],
+)
+def test_successful_initialization_with_topography(grid_fixture, request):
+    grid = request.getfixturevalue(grid_fixture)
+    assert grid is not None
+
 
+def test_plot():
     grid = Grid(
         nx=20, ny=20, size_x=100, size_y=100, center_lon=-20, center_lat=0, rot=0
     )
 
-    grid.plot(bathymetry=True)
+    grid.plot(with_dim_names=False)
+    grid.plot(with_dim_names=True)
+
+
+def test_save(tmp_path):
+    grid = Grid(
+        nx=20, ny=20, size_x=100, size_y=100, center_lon=-20, center_lat=0, rot=0
+    )
 
     for file_str in ["test_grid", "test_grid.nc"]:
         # Create a temporary filepath using the tmp_path fixture
@@ -89,7 +197,6 @@ def test_plot_save_methods(tmp_path):
             tmp_path / file_str,
             str(tmp_path / file_str),
         ]:  # test for Path object and str
-
             saved_filenames = grid.save(filepath)
             # Check if the .nc file was created
             filepath = Path(filepath).with_suffix(".nc")
@@ -102,7 +209,23 @@ def test_plot_save_methods(tmp_path):
 
 def test_raise_if_domain_too_large():
     with pytest.raises(ValueError, match="Domain size exceeds"):
-        Grid(nx=3, ny=3, size_x=30000, size_y=30000, center_lon=0, center_lat=51.5)
+        Grid(
+            nx=3,
+            ny=3,
+            size_x=MAXIMUM_GRID_SIZE + 10,
+            size_y=1000,
+            center_lon=0,
+            center_lat=51.5,
+        )
+    with pytest.raises(ValueError, match="Domain size exceeds"):
+        Grid(
+            nx=3,
+            ny=3,
+            size_x=1000,
+            size_y=MAXIMUM_GRID_SIZE + 10,
+            center_lon=0,
+            center_lat=51.5,
+        )
 
     # test grid with reasonable domain size
     grid = Grid(
@@ -141,78 +264,19 @@ def test_grid_straddle_crosses_meridian():
     assert not grid.straddle
 
 
-def test_compatability_with_matlab_grid(tmp_path):
-
-    fname = download_test_data("grid_created_with_matlab.nc")
-
-    grid = Grid.from_file(fname)
-
-    assert not grid.straddle
-    assert grid.theta_s == 5.0
-    assert grid.theta_b == 2.0
-    assert grid.hc == 300.0
-    assert grid.N == 100
-    assert grid.nx == 24
-    assert grid.ny == 24
-    assert grid.center_lon == -4.1
-    assert grid.center_lat == 52.4
-    assert grid.rot == 0.0
-
-    expected_coords = set(
-        [
-            "lat_rho",
-            "lon_rho",
-            "lat_u",
-            "lon_u",
-            "lat_v",
-            "lon_v",
-            "lat_coarse",
-            "lon_coarse",
-        ]
-    )
-    actual_coords = set(grid.ds.coords.keys())
-    assert actual_coords == expected_coords
-
-    grid.plot(bathymetry=True)
-
-    for file_str in ["test_grid", "test_grid.nc"]:
-        # Create a temporary filepath using the tmp_path fixture
-        for filepath in [
-            tmp_path / file_str,
-            str(tmp_path / file_str),
-        ]:  # test for Path object and str
-
-            # Test saving without partitioning
-            _ = grid.save(filepath)
-
-            filepath = Path(filepath)
-
-            # Load the grid from the file
-            grid_from_file = Grid.from_file(filepath.with_suffix(".nc"))
-
-            # Assert that the initial grid and the loaded grid are equivalent (including the 'ds' attribute)
-            assert grid == grid_from_file
-
-            # Clean up the .nc file
-            (filepath.with_suffix(".nc")).unlink()
-
-
-def test_roundtrip_netcdf(tmp_path):
+@pytest.mark.parametrize(
+    "grid_fixture",
+    [
+        "grid",
+        "grid_that_straddles_dateline_with_shifted_global_etopo_data",
+        "grid_that_straddles_dateline_with_global_srtm15_data",
+    ],
+)
+def test_roundtrip_netcdf(grid_fixture, tmp_path, request):
     """Test that creating a grid, saving it to file, and re-opening it is the same as
-    just creating it."""
-
-    # Initialize a Grid object using the initializer
-    grid_init = Grid(
-        nx=10,
-        ny=15,
-        size_x=100.0,
-        size_y=150.0,
-        center_lon=0.0,
-        center_lat=0.0,
-        rot=0.0,
-        topography_source={"name": "ETOPO5"},
-        hmin=5.0,
-    )
+    just creating it.
+    """
+    grid = request.getfixturevalue(grid_fixture)
 
     for file_str in ["test_grid", "test_grid.nc"]:
         # Create a temporary filepath using the tmp_path fixture
@@ -220,8 +284,7 @@ def test_roundtrip_netcdf(tmp_path):
             tmp_path / file_str,
             str(tmp_path / file_str),
         ]:  # test for Path object and str
-
-            grid_init.save(filepath)
+            grid.save(filepath)
 
             filepath = Path(filepath)
 
@@ -229,28 +292,25 @@ def test_roundtrip_netcdf(tmp_path):
             grid_from_file = Grid.from_file(filepath.with_suffix(".nc"))
 
             # Assert that the initial grid and the loaded grid are equivalent (including the 'ds' attribute)
-            assert grid_init == grid_from_file
+            assert grid == grid_from_file
 
             # Clean up the .nc file
             (filepath.with_suffix(".nc")).unlink()
 
 
-def test_roundtrip_yaml(tmp_path):
-    """Test that creating a grid, saving its parameters to yaml file, and re- opening
-    yaml file creates the same grid."""
-
-    # Initialize a Grid object using the initializer
-    grid_init = Grid(
-        nx=10,
-        ny=15,
-        size_x=100.0,
-        size_y=150.0,
-        center_lon=0.0,
-        center_lat=0.0,
-        rot=0.0,
-        topography_source={"name": "ETOPO5"},
-        hmin=5.0,
-    )
+@pytest.mark.parametrize(
+    "grid_fixture",
+    [
+        "grid",
+        "grid_that_straddles_dateline_with_shifted_global_etopo_data",
+        "grid_that_straddles_dateline_with_global_srtm15_data",
+    ],
+)
+def test_roundtrip_yaml(grid_fixture, tmp_path, request):
+    """Test that creating a grid, saving its parameters to yaml file, and re-opening
+    yaml file creates the same grid.
+    """
+    grid = request.getfixturevalue(grid_fixture)
 
     # Create a temporary filepath using the tmp_path fixture
     file_str = "test_yaml"
@@ -258,20 +318,42 @@ def test_roundtrip_yaml(tmp_path):
         tmp_path / file_str,
         str(tmp_path / file_str),
     ]:  # test for Path object and str
-
-        grid_init.to_yaml(filepath)
+        grid.to_yaml(filepath)
 
         grid_from_file = Grid.from_yaml(filepath)
 
         # Assert that the initial grid and the loaded grid are equivalent (including the 'ds' attribute)
-        assert grid_init == grid_from_file
+        assert grid == grid_from_file
 
         filepath = Path(filepath)
         filepath.unlink()
 
 
-def test_files_have_same_hash(tmp_path):
+@pytest.mark.parametrize(
+    "grid_fixture",
+    [
+        "grid",
+        "grid_that_straddles_dateline_with_shifted_global_etopo_data",
+        "grid_that_straddles_dateline_with_global_srtm15_data",
+    ],
+)
+def test_roundtrip_from_file_yaml(grid_fixture, tmp_path, request):
+    """Test that reading a grid from file and then saving it to yaml works."""
+    grid = request.getfixturevalue(grid_fixture)
+
+    filepath = Path(tmp_path / "test.nc")
+    grid.save(filepath)
+
+    grid_from_file = Grid.from_file(filepath)
+
+    filepath_yaml = Path(tmp_path / "test.yaml")
+    grid_from_file.to_yaml(filepath_yaml)
 
+    filepath.unlink()
+    filepath_yaml.unlink()
+
+
+def test_files_have_same_hash(tmp_path):
     # Initialize a Grid object using the initializer
     grid_init = Grid(
         nx=10,
@@ -306,7 +388,6 @@ def test_files_have_same_hash(tmp_path):
 
 
 def test_from_yaml_missing_version(tmp_path):
-
     yaml_content = textwrap.dedent(
         """\
     Grid:
@@ -328,7 +409,6 @@ def test_from_yaml_missing_version(tmp_path):
         tmp_path / file_str,
         str(tmp_path / file_str),
     ]:  # test for Path object and str
-
         # Write YAML content to file
         if isinstance(yaml_filepath, Path):
             yaml_filepath.write_text(yaml_content)
@@ -356,7 +436,6 @@ def test_from_yaml_missing_grid(tmp_path):
         tmp_path / file_str,
         str(tmp_path / file_str),
     ]:  # test for Path object and str
-
         # Write YAML content to file
         if isinstance(yaml_filepath, Path):
             yaml_filepath.write_text(yaml_content)
@@ -399,7 +478,6 @@ def test_from_yaml_version_mismatch(tmp_path, caplog):
         tmp_path / file_str,
         str(tmp_path / file_str),
     ]:  # test for Path object and str
-
         # Write YAML content to file
         if isinstance(yaml_filepath, Path):
             yaml_filepath.write_text(yaml_content)
@@ -420,7 +498,6 @@ def test_from_yaml_version_mismatch(tmp_path, caplog):
 def test_invalid_theta_s_value():
     """Test the validation of the theta_s value."""
     with pytest.raises(ValueError):
-
         Grid(
             nx=2,
             ny=2,
@@ -430,9 +507,7 @@ def test_invalid_theta_s_value():
             center_lat=55,
             rot=10,
             N=3,
-            theta_s=11.0,  # Invalid value, should be 0 < theta_s <= 10
-            theta_b=2.0,
-            hc=250.0,
+            theta_s=UPPER_BOUND_THETA_S + 1,
         )
 
 
@@ -448,14 +523,11 @@ def test_invalid_theta_b_value():
             center_lat=55,
             rot=10,
             N=3,
-            theta_s=5.0,
-            theta_b=5.0,  # Invalid value, should be 0 < theta_b <= 4
-            hc=250.0,
+            theta_b=UPPER_BOUND_THETA_B + 1,
         )
 
 
 def test_update_vertical_coordinate():
-
     grid = Grid(
         nx=2, ny=2, size_x=500, size_y=1000, center_lon=0, center_lat=55, rot=10
     )
@@ -491,7 +563,7 @@ def test_update_vertical_coordinate():
     assert len(grid.ds.s_rho) == 5
 
 
-def test_plot():
+def test_plot_vertical_coordinate():
     grid = Grid(
         nx=2,
         ny=2,
@@ -508,6 +580,13 @@ def test_plot():
     grid.plot_vertical_coordinate(s=-1)
     grid.plot_vertical_coordinate(eta=0)
     grid.plot_vertical_coordinate(xi=0)
+    # Test that passing a maximum number of layer contours works
+    grid.plot_vertical_coordinate(xi=0, max_nr_layer_contours=2)
+    grid.plot_vertical_coordinate(xi=0, max_nr_layer_contours=100)
+    # Test that passing a matplotlib.axes.Axes works
+    fig, ax = plt.subplots(1, 1)
+    grid.plot_vertical_coordinate(s=-1, ax=ax)
+    grid.plot_vertical_coordinate(eta=0, ax=ax)
 
     with pytest.raises(ValueError, match="Exactly one of"):
         grid.plot_vertical_coordinate(s=-1, eta=0)
@@ -517,3 +596,217 @@ def test_plot():
         grid.plot_vertical_coordinate(eta=-1, xi=0)
     with pytest.raises(ValueError, match="Exactly one of"):
         grid.plot_vertical_coordinate(eta=-1, xi=0, s=-1)
+
+
+# More Grid.from_file() tests
+
+
+def test_compatability_with_matlab_grid(tmp_path):
+    fname = download_test_data("grid_created_with_matlab.nc")
+
+    grid = Grid.from_file(fname)
+
+    assert not grid.straddle
+    assert grid.theta_s == 5.0
+    assert grid.theta_b == 2.0
+    assert grid.hc == 300.0
+    assert grid.N == 100
+    assert grid.nx == 24
+    assert grid.ny == 24
+    assert grid.center_lon == -4.1
+    assert grid.center_lat == 52.4
+    assert grid.rot == 0.0
+
+    expected_coords = set(
+        [
+            "lat_rho",
+            "lon_rho",
+            "lat_u",
+            "lon_u",
+            "lat_v",
+            "lon_v",
+            "lat_coarse",
+            "lon_coarse",
+        ]
+    )
+    actual_coords = set(grid.ds.coords.keys())
+    assert actual_coords == expected_coords
+
+    grid.plot()
+
+    for file_str in ["test_grid", "test_grid.nc"]:
+        # Create a temporary filepath using the tmp_path fixture
+        for filepath in [
+            tmp_path / file_str,
+            str(tmp_path / file_str),
+        ]:  # test for Path object and str
+            # Test saving without partitioning
+            _ = grid.save(filepath)
+
+            filepath = Path(filepath)
+
+            # Load the grid from the file
+            grid_from_file = Grid.from_file(filepath.with_suffix(".nc"))
+
+            # Assert that the initial grid and the loaded grid are equivalent (including the 'ds' attribute)
+            assert grid == grid_from_file
+
+            # Clean up the .nc file
+            (filepath.with_suffix(".nc")).unlink()
+
+
+def test_from_file_with_vertical_coords(grid, tmp_path):
+    theta_s = 6.0
+    theta_b = 4.0
+    hc = 300.0
+    N = 10
+
+    grid_copy = copy.deepcopy(grid)
+    grid_copy.update_vertical_coordinate(theta_s=theta_s, theta_b=theta_b, hc=hc, N=N)
+    Cs_r = grid_copy.ds.Cs_r
+    Cs_w = grid_copy.ds.Cs_w
+    path = tmp_path / "grid.nc"
+    grid_copy.save(path)
+
+    grid_from_file = Grid.from_file(path, theta_s=theta_s, theta_b=theta_b, hc=hc, N=N)
+    assert np.allclose(grid_from_file.ds.Cs_r, Cs_r)
+    assert np.allclose(grid_from_file.ds.Cs_w, Cs_w)
+    assert grid_from_file.theta_s == theta_s
+    assert grid_from_file.theta_b == theta_b
+    assert grid_from_file.hc == hc
+    assert grid_from_file.N == N
+
+
+def test_from_file_with_conflicting_vertical_coords(grid, tmp_path):
+    theta_s = 6.0
+    theta_b = 4.0
+    hc = 300.0
+    N = 10
+
+    grid_copy = copy.deepcopy(grid)
+    grid_copy.update_vertical_coordinate(theta_s=theta_s, theta_b=theta_b, hc=hc, N=N)
+
+    path = tmp_path / "grid.nc"
+    grid_copy.save(path)
+
+    with pytest.raises(ValueError, match="inconsistent with the provided N"):
+        Grid.from_file(path, theta_s=5.0, theta_b=2.0, hc=300.0, N=100)
+
+    with pytest.raises(ValueError, match="inconsistent with the provided theta_s, "):
+        Grid.from_file(path, theta_s=5.0, theta_b=2.0, hc=300.0, N=10)
+
+
+def test_from_file_missing_attributes(grid, tmp_path):
+    grid_copy = copy.deepcopy(grid)
+    del grid_copy.ds.attrs["theta_b"]
+
+    path = tmp_path / "grid.nc"
+    grid_copy.save(path)
+
+    with pytest.raises(ValueError, match="Missing vertical coordinate attributes"):
+        Grid.from_file(path)
+
+
+def test_from_file_partial_parameters_raises_error(grid, tmp_path):
+    path = tmp_path / "grid.nc"
+    grid.save(path)
+
+    with pytest.raises(ValueError, match="must provide all of"):
+        Grid.from_file(path, theta_s=5.0)
+
+
+# Topography tests
+def test_enclosed_regions():
+    """Test that there are only two connected regions, one dry and one wet."""
+    grid = Grid(
+        nx=100,
+        ny=100,
+        size_x=1800,
+        size_y=2400,
+        center_lon=30,
+        center_lat=61,
+        rot=20,
+    )
+
+    reg, nreg = label(grid.ds.mask_rho)
+    npt.assert_equal(nreg, 2)
+
+
+def test_rmax_criterion():
+    grid = Grid(
+        nx=100,
+        ny=100,
+        size_x=1800,
+        size_y=2400,
+        center_lon=30,
+        center_lat=61,
+        rot=20,
+    )
+    r_eta, r_xi = _compute_rfactor(grid.ds.h)
+    rmax0 = np.max([r_eta.max(), r_xi.max()])
+    npt.assert_array_less(rmax0, 0.2)
+
+
+def test_hmin_criterion():
+    grid = Grid(
+        nx=100,
+        ny=100,
+        size_x=1800,
+        size_y=2400,
+        center_lon=30,
+        center_lat=61,
+        rot=20,
+        hmin=5.0,
+    )
+
+    assert grid.hmin == 5.0
+    assert np.less_equal(grid.hmin, grid.ds.h.min())
+
+    grid.update_topography(hmin=10.0)
+
+    assert grid.hmin == 10.0
+    assert np.less_equal(grid.hmin, grid.ds.h.min())
+
+    # this should not do anything
+    grid.update_topography()
+
+    assert grid.hmin == 10.0
+    assert np.less_equal(grid.hmin, grid.ds.h.min())
+
+
+def test_mask_topography_boundary():
+    """Test that the mask and topography along the grid boundaries (north, south, east,
+    west) are identical to the adjacent inland cells.
+    """
+    # Create a grid with some land along the northern boundary
+    grid = Grid(
+        nx=10, ny=10, size_x=1000, size_y=1000, center_lon=-20, center_lat=60, rot=0
+    )
+
+    # Toopography
+    np.testing.assert_array_equal(
+        grid.ds.h.isel(eta_rho=0).data, grid.ds.h.isel(eta_rho=1).data
+    )
+    np.testing.assert_array_equal(
+        grid.ds.h.isel(eta_rho=-1).data, grid.ds.h.isel(eta_rho=-2).data
+    )
+    np.testing.assert_array_equal(
+        grid.ds.h.isel(xi_rho=0).data, grid.ds.h.isel(xi_rho=1).data
+    )
+    np.testing.assert_array_equal(
+        grid.ds.h.isel(xi_rho=-1).data, grid.ds.h.isel(xi_rho=-2).data
+    )
+
+    # Mask
+    np.testing.assert_array_equal(
+        grid.ds.mask_rho.isel(eta_rho=0).data, grid.ds.mask_rho.isel(eta_rho=1).data
+    )
+    np.testing.assert_array_equal(
+        grid.ds.mask_rho.isel(eta_rho=-1).data, grid.ds.mask_rho.isel(eta_rho=-2).data
+    )
+    np.testing.assert_array_equal(
+        grid.ds.mask_rho.isel(xi_rho=0).data, grid.ds.mask_rho.isel(xi_rho=1).data
+    )
+    np.testing.assert_array_equal(
+        grid.ds.mask_rho.isel(xi_rho=-1).data, grid.ds.mask_rho.isel(xi_rho=-2).data
+    )