diff --git a/docs/src/conf.py b/docs/src/conf.py index f5d0d37c21..2fb62b256e 100644 --- a/docs/src/conf.py +++ b/docs/src/conf.py @@ -252,6 +252,8 @@ def _dotv(version): "scipy": ("https://docs.scipy.org/doc/scipy/", None), "pandas": ("https://pandas.pydata.org/docs/", None), "dask": ("https://docs.dask.org/en/stable/", None), + "geovista": ("https://geovista.readthedocs.io/en/latest/", None), + "pyvista": ("https://docs.pyvista.org/", None), } # The name of the Pygments (syntax highlighting) style to use. diff --git a/docs/src/further_topics/ugrid/images/plotting.png b/docs/src/further_topics/ugrid/images/plotting.png new file mode 100644 index 0000000000..6e7d570ba2 Binary files /dev/null and b/docs/src/further_topics/ugrid/images/plotting.png differ diff --git a/docs/src/further_topics/ugrid/images/plotting_basic.png b/docs/src/further_topics/ugrid/images/plotting_basic.png deleted file mode 100644 index ba2b0b3329..0000000000 Binary files a/docs/src/further_topics/ugrid/images/plotting_basic.png and /dev/null differ diff --git a/docs/src/further_topics/ugrid/images/plotting_global.png b/docs/src/further_topics/ugrid/images/plotting_global.png deleted file mode 100644 index 62fb56d974..0000000000 Binary files a/docs/src/further_topics/ugrid/images/plotting_global.png and /dev/null differ diff --git a/docs/src/further_topics/ugrid/operations.rst b/docs/src/further_topics/ugrid/operations.rst index a088b588e1..8c01b8eae5 100644 --- a/docs/src/further_topics/ugrid/operations.rst +++ b/docs/src/further_topics/ugrid/operations.rst @@ -469,14 +469,18 @@ SEM microscopy), so there is a wealth of tooling available, which :ref:`ugrid geovista` harnesses for cartographic plotting. GeoVista's default behaviour is to convert lat-lon information into full XYZ -coordinates so the data is visualised on the surface of a 3D globe. The plots -are interactive by default, so it's easy to explore the data in detail. +coordinates so the data is visualised on the surface of a 3D globe; 2D +projections are also supported. The plots are interactive by default, so it's +easy to explore the data in detail. -2D projections have also been demonstrated in proofs of concept, and will -be added to API in the near future. +Performing GeoVista operations on your :class:`~iris.cube.Cube` is made +easy via this convenience: +:func:`iris.experimental.geovista.cube_to_polydata`. -This first example uses GeoVista to plot the ``face_cube`` that we created -earlier: +Below is an example of using GeoVista to plot a low-res +sample :attr:`~iris.cube.Cube.mesh` based :class:`~iris.cube.Cube`. For +some truly spectacular visualisations of high-res data please see the +GeoVista :external+geovista:doc:`generated/gallery/index`. .. dropdown:: Code :icon: code @@ -484,130 +488,48 @@ earlier: .. code-block:: python >>> from geovista import GeoPlotter, Transform - >>> from geovista.common import to_xyz + >>> from geovista.common import to_cartesian + >>> import matplotlib.pyplot as plt + >>> from iris import load_cube, sample_data_path + >>> from iris.experimental.geovista import cube_to_polydata + >>> from iris.experimental.ugrid import PARSE_UGRID_ON_LOAD - # We'll re-use this to plot some real global data later. - >>> def cube_faces_to_polydata(cube): - ... lons, lats = cube.mesh.node_coords - ... face_node = cube.mesh.face_node_connectivity - ... indices = face_node.indices_by_location() - ... - ... mesh = Transform.from_unstructured( - ... lons.points, - ... lats.points, - ... indices, - ... data=cube.data, - ... name=f"{cube.name()} / {cube.units}", - ... start_index=face_node.start_index, - ... ) - ... return mesh - - >>> print(face_cube) - face_data / (K) (-- : 2; height: 3) - Dimension coordinates: - height - x + >>> with PARSE_UGRID_ON_LOAD.context(): + ... sample_mesh_cube = load_cube(sample_data_path("mesh_C4_synthetic_float.nc")) + >>> print(sample_mesh_cube) + synthetic / (1) (-- : 96) Mesh coordinates: - latitude x - - longitude x - + latitude x + longitude x + Mesh: + name Topology data of 2D unstructured mesh + location face Attributes: - Conventions 'CF-1.7' + NCO 'netCDF Operators version 4.7.5 (Homepage = http://nco.sf.net, Code = h ...' + history 'Mon Apr 12 01:44:41 2021: ncap2 -s synthetic=float(synthetic) mesh_C4_synthetic.nc ...' + nco_openmp_thread_number 1 # Convert our mesh+data to a PolyData object. - # Just plotting a single height level. - >>> face_polydata = cube_faces_to_polydata(face_cube[:, 0]) + >>> face_polydata = cube_to_polydata(sample_mesh_cube) >>> print(face_polydata) - PolyData (0x7ff4861ff4c0) - N Cells: 2 - N Points: 5 - X Bounds: 9.903e-01, 1.000e+00 - Y Bounds: 0.000e+00, 1.392e-01 - Z Bounds: 6.123e-17, 5.234e-02 - N Arrays: 2 + PolyData (... + N Cells: 96 + N Points: 98 + N Strips: 0 + X Bounds: -1.000e+00, 1.000e+00 + Y Bounds: -1.000e+00, 1.000e+00 + Z Bounds: -1.000e+00, 1.000e+00 + N Arrays: 4 # Create the GeoVista plotter and add our mesh+data to it. - >>> my_plotter = GeoPlotter() - >>> my_plotter.add_coastlines(color="black") - >>> my_plotter.add_base_layer(color="grey") - >>> my_plotter.add_mesh(face_polydata) - - # Centre the camera on the data. - >>> camera_region = to_xyz( - ... face_cube.coord("longitude").points, - ... face_cube.coord("latitude").points, - ... radius=3, - ... ) - >>> camera_pos = camera_region.mean(axis=0) - >>> my_plotter.camera.position = camera_pos - - >>> my_plotter.show() - - .. image:: images/plotting_basic.png - :alt: A GeoVista plot of the basic example Mesh. - - This artificial data makes West Africa rather chilly! - -Here's another example using a global cubed-sphere data set: - -.. dropdown:: Code - :icon: code - - .. code-block:: python - - >>> from iris import load_cube - >>> from iris.experimental.ugrid import PARSE_UGRID_ON_LOAD - - # Demonstrating with a global data set. - # You could also download this file from github.com/SciTools/iris-test-data. - >>> from iris.tests import get_data_path - >>> file_path = get_data_path( - ... [ - ... "NetCDF", - ... "unstructured_grid", - ... "lfric_surface_mean.nc", - ... ] - ... ) - >>> with PARSE_UGRID_ON_LOAD.context(): - ... global_cube = load_cube(file_path, "tstar_sea") - >>> print(global_cube) - sea_surface_temperature / (K) (-- : 1; -- : 13824) - Mesh coordinates: - latitude - x - longitude - x - Auxiliary coordinates: - time x - - Cell methods: - 0 time: mean (interval: 300 s) - 1 time_counter: mean - Attributes: - Conventions UGRID - description Created by xios - interval_operation 300 s - interval_write 1 d - name lfric_surface - online_operation average - timeStamp 2020-Feb-07 16:23:14 GMT - title Created by xios - uuid 489bcef5-3d1c-4529-be42-4ab5f8c8497b - - >>> global_polydata = cube_faces_to_polydata(global_cube) - >>> print(global_polydata) - PolyData (0x7f761b536160) - N Cells: 13824 - N Points: 13826 - X Bounds: -1.000e+00, 1.000e+00 - Y Bounds: -1.000e+00, 1.000e+00 - Z Bounds: -1.000e+00, 1.000e+00 - N Arrays: 2 - >>> my_plotter = GeoPlotter() >>> my_plotter.add_coastlines() - >>> my_plotter.add_mesh(global_polydata, show_edges=True) - + >>> my_plotter.add_mesh(face_polydata) >>> my_plotter.show() - .. image:: images/plotting_global.png - :alt: A GeoVista plot of a global sea surface temperature Mesh. + .. image:: images/plotting.png + :alt: A GeoVista plot of low-res sample data. Region Extraction ----------------- @@ -656,118 +578,59 @@ position of the data points before they can be analysed as inside/outside the selected region. The recommended way to do this is using tools provided by :ref:`ugrid geovista`, which is optimised for performant mesh analysis. -This approach centres around using :meth:`geovista.geodesic.BBox.enclosed` to -get the subset of the original mesh that is inside the -:class:`~geovista.geodesic.BBox`. This subset :class:`pyvista.PolyData` object -includes the original indices of each datapoint - the ``vtkOriginalCellIds`` -array, which can be used to index the original :class:`~iris.cube.Cube`. Since -we **know** that this subset :class:`~iris.cube.Cube` represents a regional -mesh, we then reconstruct a :class:`~iris.experimental.ugrid.Mesh` from the -:class:`~iris.cube.Cube`\'s :attr:`~iris.cube.Cube.aux_coords` using -:meth:`iris.experimental.ugrid.Mesh.from_coords`: +Performing GeoVista operations on your :class:`~iris.cube.Cube` is made +easy via this convenience: +:func:`iris.experimental.geovista.cube_to_polydata`. + +An Iris convenience for regional extraction is also provided: +:func:`iris.experimental.geovista.extract_unstructured_region`; demonstrated +below: -.. - Not using doctest here as want to keep GeoVista as optional dependency. .. dropdown:: Code :icon: code - .. code-block:: python + .. doctest:: ugrid_operations - >>> from geovista import Transform >>> from geovista.geodesic import BBox - >>> from iris import load_cube - >>> from iris.experimental.ugrid import Mesh, PARSE_UGRID_ON_LOAD - - # Need a larger dataset to demonstrate this operation. - # You could also download this file from github.com/SciTools/iris-test-data. - >>> from iris.tests import get_data_path - >>> file_path = get_data_path( - ... [ - ... "NetCDF", - ... "unstructured_grid", - ... "lfric_ngvat_2D_72t_face_half_levels_main_conv_rain.nc", - ... ] - ... ) + >>> from iris import load_cube, sample_data_path + >>> from iris.experimental.geovista import cube_to_polydata, extract_unstructured_region + >>> from iris.experimental.ugrid import PARSE_UGRID_ON_LOAD >>> with PARSE_UGRID_ON_LOAD.context(): - ... global_cube = load_cube(file_path, "conv_rain") - >>> print(global_cube) - surface_convective_rainfall_rate / (kg m-2 s-1) (-- : 72; -- : 864) + ... sample_mesh_cube = load_cube(sample_data_path("mesh_C4_synthetic_float.nc")) + >>> print(sample_mesh_cube) + synthetic / (1) (-- : 96) Mesh coordinates: - latitude - x - longitude - x - Auxiliary coordinates: - time x - - Cell methods: - 0 time: point + latitude x + longitude x + Mesh: + name Topology data of 2D unstructured mesh + location face Attributes: - Conventions UGRID - description Created by xios - interval_operation 300 s - interval_write 300 s - name lfric_ngvat_2D_72t_face_half_levels_main_conv_rain - online_operation instant - timeStamp 2020-Oct-18 21:18:35 GMT - title Created by xios - uuid b3dc0fb4-9828-4663-a5ac-2a5763280159 - - # Convert the Mesh to a GeoVista PolyData object. - >>> lons, lats = global_cube.mesh.node_coords - >>> face_node = global_cube.mesh.face_node_connectivity - >>> indices = face_node.indices_by_location() - >>> global_polydata = Transform.from_unstructured( - ... lons.points, lats.points, indices, start_index=face_node.start_index + NCO 'netCDF Operators version 4.7.5 (Homepage = http://nco.sf.net, Code = h ...' + history 'Mon Apr 12 01:44:41 2021: ncap2 -s synthetic=float(synthetic) mesh_C4_synthetic.nc ...' + nco_openmp_thread_number 1 + + >>> regional_cube = extract_unstructured_region( + ... cube=sample_mesh_cube, + ... polydata=cube_to_polydata(sample_mesh_cube), + ... region=BBox(lons=[0, 70, 70, 0], lats=[-25, -25, 45, 45]), + ... preference="center", ... ) - - # Define a region of 4 corners connected by great circles. - # Specialised sub-classes of BBox are also available e.g. panel/wedge. - >>> region = BBox(lons=[0, 70, 70, 0], lats=[-25, -25, 45, 45]) - # 'Apply' the region to the PolyData object. - >>> region_polydata = region.enclosed(global_polydata, preference="center") - # Get the remaining face indices, to use for indexing the Cube. - >>> indices = region_polydata["vtkOriginalCellIds"] - - >>> print(type(indices)) - - # 101 is smaller than the original 864. - >>> print(len(indices)) - 101 - >>> print(indices[:10]) - [ 6 7 8 9 10 11 18 19 20 21] - - # Use the face indices to subset the global cube. - >>> region_cube = global_cube[:, indices] - - # In this case we **know** the indices correspond to a contiguous - # region, so we will convert the sub-setted Cube back into a - # Cube-with-Mesh. - >>> new_mesh = Mesh.from_coords(*region_cube.coords(dimensions=1)) - >>> new_mesh_coords = new_mesh.to_MeshCoords(global_cube.location) - >>> for coord in new_mesh_coords: - ... region_cube.remove_coord(coord.name()) - ... region_cube.add_aux_coord(coord, 1) - - # A Mesh-Cube with a subset (101) of the original 864 faces. - >>> print(region_cube) - surface_convective_rainfall_rate / (kg m-2 s-1) (-- : 72; -- : 101) + >>> print(regional_cube) + synthetic / (1) (-- : 11) Mesh coordinates: - latitude - x - longitude - x - Auxiliary coordinates: - time x - - Cell methods: - 0 time: point + latitude x + longitude x + Mesh: + name unknown + location face Attributes: - Conventions UGRID - description Created by xios - interval_operation 300 s - interval_write 300 s - name lfric_ngvat_2D_72t_face_half_levels_main_conv_rain - online_operation instant - timeStamp 2020-Oct-18 21:18:35 GMT - title Created by xios - uuid b3dc0fb4-9828-4663-a5ac-2a5763280159 + NCO 'netCDF Operators version 4.7.5 (Homepage = http://nco.sf.net, Code = h ...' + history 'Mon Apr 12 01:44:41 2021: ncap2 -s synthetic=float(synthetic) mesh_C4_synthetic.nc ...' + nco_openmp_thread_number 1 + Regridding ---------- @@ -1029,4 +892,4 @@ data content. .. |new| replace:: ✨ New .. |unchanged| replace:: ♻️ Unchanged .. |different| replace:: ⚠️ Different -.. |pending| replace:: 🚧 Support Pending \ No newline at end of file +.. |pending| replace:: 🚧 Support Pending diff --git a/lib/iris/experimental/geovista.py b/lib/iris/experimental/geovista.py new file mode 100644 index 0000000000..26bfa2e703 --- /dev/null +++ b/lib/iris/experimental/geovista.py @@ -0,0 +1,339 @@ +# Copyright Iris contributors +# +# This file is part of Iris and is released under the BSD license. +# See LICENSE in the root of the repository for full licensing details. +"""Experimental module for using some GeoVista operations with Iris cubes.""" + +from geovista import Transform +from geovista.common import VTK_CELL_IDS, VTK_POINT_IDS + +from iris.exceptions import CoordinateNotFoundError +from iris.experimental.ugrid import Mesh + + +def _get_coord(cube, axis): + """Get the axis coordinates from the cube.""" + try: + coord = cube.coord(axis=axis, dim_coords=True) + except CoordinateNotFoundError: + coord = cube.coord(axis=axis) + return coord + + +def cube_to_polydata(cube, **kwargs): + r"""Create a :class:`pyvista.PolyData` object from a :class:`~iris.cube.Cube`. + + The resulting :class:`~pyvista.PolyData` object can be plotted using + a :class:`geovista.geoplotter.GeoPlotter`. + + Uses :class:`geovista.bridge.Transform` to parse the cube's information - one + of: :meth:`~geovista.bridge.Transform.from_1d` / + :meth:`~geovista.bridge.Transform.from_2d` / + :meth:`~geovista.bridge.Transform.from_unstructured`. + + Parameters + ---------- + cube : :class:`~iris.cube.Cube` + The Cube containing the spatial information and data for creating the + class:`~pyvista.PolyData`. + + **kwargs : dict, optional + Additional keyword arguments to be passed to the relevant + :class:`~geovista.bridge.Transform` method (e.g ``zlevel``). + + Returns + ------- + :class:`~pyvista.PolyData` + The PolyData object representing the cube's spatial information and data. + + Raises + ------ + NotImplementedError + If a :class:`~iris.cube.Cube` with too many dimensions is passed. Only + the horizontal data can be represented, meaning a 2D Cube, or 1D Cube + if the horizontal space is described by + :class:`~iris.experimental.ugrid.MeshCoord`\ s. + + Examples + -------- + .. testsetup:: + + from iris import load_cube, sample_data_path + from iris.experimental.ugrid import PARSE_UGRID_ON_LOAD + + cube = load_cube(sample_data_path("air_temp.pp")) + cube_w_time = load_cube(sample_data_path("A1B_north_america.nc")) + with PARSE_UGRID_ON_LOAD.context(): + cube_mesh = load_cube(sample_data_path("mesh_C4_synthetic_float.nc")) + + >>> from iris.experimental.geovista import cube_to_polydata + + Converting a standard 2-dimensional :class:`~iris.cube.Cube` with + 1-dimensional coordinates: + + >>> print(cube.summary(shorten=True)) + air_temperature / (K) (latitude: 73; longitude: 96) + >>> print(cube_to_polydata(cube)) + PolyData (... + N Cells: 7008 + N Points: 7178 + N Strips: 0 + X Bounds: -9.992e-01, 9.992e-01 + Y Bounds: -9.992e-01, 9.992e-01 + Z Bounds: -1.000e+00, 1.000e+00 + N Arrays: 4 + + Configure the conversion by passing additional keyword arguments: + + >>> print(cube_to_polydata(cube, radius=2)) + PolyData (... + N Cells: 7008 + N Points: 7178 + N Strips: 0 + X Bounds: -1.998e+00, 1.998e+00 + Y Bounds: -1.998e+00, 1.998e+00 + Z Bounds: -2.000e+00, 2.000e+00 + N Arrays: 4 + + Converting a :class:`~iris.cube.Cube` that has a + :attr:`~iris.cube.Cube.mesh` describing its horizontal space: + + >>> print(cube_mesh.summary(shorten=True)) + synthetic / (1) (-- : 96) + >>> print(cube_to_polydata(cube_mesh)) + PolyData (... + N Cells: 96 + N Points: 98 + N Strips: 0 + X Bounds: -1.000e+00, 1.000e+00 + Y Bounds: -1.000e+00, 1.000e+00 + Z Bounds: -1.000e+00, 1.000e+00 + N Arrays: 4 + + Remember to reduce the dimensionality of your :class:`~iris.cube.Cube` to + just be the horizontal space: + + >>> print(cube_w_time.summary(shorten=True)) + air_temperature / (K) (time: 240; latitude: 37; longitude: 49) + >>> print(cube_to_polydata(cube_w_time[0, :, :])) + PolyData (... + N Cells: 1813 + N Points: 1900 + N Strips: 0 + X Bounds: -6.961e-01, 6.961e-01 + Y Bounds: -9.686e-01, -3.411e-01 + Z Bounds: 2.483e-01, 8.714e-01 + N Arrays: 4 + + """ + if cube.mesh: + if cube.ndim != 1: + raise NotImplementedError("Cubes with a mesh must be one dimensional") + lons, lats = cube.mesh.node_coords + face_node = cube.mesh.face_node_connectivity + indices = face_node.indices_by_location() + + polydata = Transform.from_unstructured( + xs=lons.points, + ys=lats.points, + connectivity=indices, + data=cube.data, + name=f"{cube.name()} / ({cube.units})", + start_index=face_node.start_index, + **kwargs, + ) + # TODO: Add support for point clouds + elif cube.ndim == 2: + x_coord = _get_coord(cube, "X") + y_coord = _get_coord(cube, "Y") + transform_kwargs = dict( + xs=x_coord.contiguous_bounds(), + ys=y_coord.contiguous_bounds(), + data=cube.data, + name=f"{cube.name()} / ({cube.units})", + **kwargs, + ) + coord_system = cube.coord_system() + if coord_system: + transform_kwargs["crs"] = coord_system.as_cartopy_crs().proj4_init + + if x_coord.ndim == 2 and y_coord.ndim == 2: + polydata = Transform.from_2d(**transform_kwargs) + + elif x_coord.ndim == 1 and y_coord.ndim == 1: + polydata = Transform.from_1d(**transform_kwargs) + + else: + raise NotImplementedError("Only 1D and 2D coordinates are supported") + else: + raise NotImplementedError("Cube must have a mesh or have 2 dimensions") + + return polydata + + +def extract_unstructured_region(cube, polydata, region, **kwargs): + """Index a :class:`~iris.cube.Cube` with a :attr:`~iris.cube.Cube.mesh` to a specific region. + + Uses :meth:`geovista.geodesic.BBox.enclosed` to identify the `cube` indices + that are within the specified region (`region` being a + :class:`~geovista.geodesic.BBox` class). + + Parameters + ---------- + cube : :class:`~iris.cube.Cube` + The cube to be indexed (must have a :attr:`~iris.cube.Cube.mesh`). + polydata : :class:`pyvista.PolyData` + A :class:`~pyvista.PolyData` representing the same horizontal space as + `cube`. The region extraction is first applied to `polydata`, with the + resulting indices then applied to `cube`. In many cases `polydata` can + be created by applying :func:`cube_to_polydata` to `cube`. + region : :class:`geovista.geodesic.BBox` + A :class:`~geovista.geodesic.BBox` representing the region to be + extracted. + **kwargs : dict, optional + Additional keyword arguments to be passed to the + :meth:`geovista.geodesic.BBox.enclosed` method (e.g ``preference``). + + Returns + ------- + :class:`~iris.cube.Cube` + The region extracted cube. + + Raises + ------ + ValueError + If `polydata` and the :attr:`~iris.cube.Cube.mesh` on `cube` do not + have the same shape. + + Examples + -------- + .. testsetup:: + + from iris import load_cube, sample_data_path + from iris.coords import AuxCoord + from iris.cube import CubeList + from iris.experimental.ugrid import PARSE_UGRID_ON_LOAD + + file_path = sample_data_path("mesh_C4_synthetic_float.nc") + with PARSE_UGRID_ON_LOAD.context(): + cube_w_mesh = load_cube(file_path) + + level_cubes = CubeList() + for height_level in range(72): + height_coord = AuxCoord([height_level], standard_name="height") + level_cube = cube_w_mesh.copy() + level_cube.add_aux_coord(height_coord) + level_cubes.append(level_cube) + + cube_w_mesh = level_cubes.merge_cube() + other_cube_w_mesh = cube_w_mesh[:20, :] + + The parameters of :func:`extract_unstructured_region` have been designed with + flexibility and reuse in mind. This is demonstrated below. + + >>> from geovista import BBox + >>> from iris.experimental.geovista import cube_to_polydata, extract_unstructured_region + >>> print(cube_w_mesh.shape) + (72, 96) + >>> # The mesh dimension represents the horizontal space of the cube. + >>> print(cube_w_mesh.shape[cube_w_mesh.mesh_dim()]) + 96 + >>> cube_polydata = cube_to_polydata(cube_w_mesh[0, :]) + >>> extracted_cube = extract_unstructured_region( + ... cube=cube_w_mesh, + ... polydata=cube_polydata, + ... region=BBox(lons=[0, 70, 70, 0], lats=[-25, -25, 45, 45]), + ... ) + >>> print(extracted_cube.shape) + (72, 11) + + Now reuse the same `cube` and `polydata` to extract a different region: + + >>> new_region = BBox(lons=[0, 35, 35, 0], lats=[-25, -25, 45, 45]) + >>> extracted_cube = extract_unstructured_region( + ... cube=cube_w_mesh, + ... polydata=cube_polydata, + ... region=new_region, + ... ) + >>> print(extracted_cube.shape) + (72, 6) + + Now apply the same region extraction to a different `cube` that has the + same horizontal shape: + + >>> print(other_cube_w_mesh.shape) + (20, 96) + >>> extracted_cube = extract_unstructured_region( + ... cube=other_cube_w_mesh, + ... polydata=cube_polydata, + ... region=new_region, + ... ) + >>> print(extracted_cube.shape) + (20, 6) + + Arbitrary keywords can be passed down to + :meth:`geovista.geodesic.BBox.enclosed` (``outside`` in this example): + + >>> extracted_cube = extract_unstructured_region( + ... cube=other_cube_w_mesh, + ... polydata=cube_polydata, + ... region=new_region, + ... outside=True, + ... ) + >>> print(extracted_cube.shape) + (20, 90) + + """ + if cube.mesh: + # Find what dimension the mesh is in on the cube + mesh_dim = cube.mesh_dim() + recreate_mesh = False + + if cube.location == "face": + polydata_length = polydata.GetNumberOfCells() + indices_key = VTK_CELL_IDS + recreate_mesh = True + elif cube.location == "node": + polydata_length = polydata.GetNumberOfPoints() + indices_key = VTK_POINT_IDS + else: + raise NotImplementedError( + f"cube.location must be `face` or `node`. Found: {cube.location}." + ) + + if cube.shape[mesh_dim] != polydata_length: + raise ValueError( + f"The mesh on the cube and the polydata" + f"must have the same shape." + f" Found Mesh: {cube.shape[mesh_dim]}," + f" Polydata: {polydata_length}." + ) + + region_polydata = region.enclosed(polydata, **kwargs) + indices = region_polydata[indices_key] + if len(indices) == 0: + raise IndexError("No part of `polydata` falls within `region`.") + + my_tuple = tuple( + [slice(None) if i != mesh_dim else indices for i in range(cube.ndim)] + ) + + region_cube = cube[my_tuple] + + if recreate_mesh: + coords_on_mesh_dim = region_cube.coords(dimensions=mesh_dim) + new_mesh = Mesh.from_coords( + *[c for c in coords_on_mesh_dim if c.has_bounds()] + ) + + new_mesh_coords = new_mesh.to_MeshCoords(cube.location) + + for coord in new_mesh_coords: + region_cube.remove_coord(coord.name()) + region_cube.add_aux_coord(coord, mesh_dim) + + # TODO: Support unstructured point based data without a mesh + else: + raise ValueError("Cube must have a mesh") + + return region_cube diff --git a/lib/iris/experimental/ugrid/mesh.py b/lib/iris/experimental/ugrid/mesh.py index a9a880813c..a798f7af77 100644 --- a/lib/iris/experimental/ugrid/mesh.py +++ b/lib/iris/experimental/ugrid/mesh.py @@ -863,6 +863,7 @@ def check_shape(array_name): ##### # TODO: remove axis assignment once Mesh supports arbitrary coords. + # TODO: consider filtering coords as the first action in this method. axes_present = [guess_coord_axis(coord) for coord in coords] axes_required = ("X", "Y") if all([req in axes_present for req in axes_required]): diff --git a/lib/iris/tests/integration/experimental/geovista/__init__.py b/lib/iris/tests/integration/experimental/geovista/__init__.py new file mode 100644 index 0000000000..6a56e09db4 --- /dev/null +++ b/lib/iris/tests/integration/experimental/geovista/__init__.py @@ -0,0 +1,5 @@ +# Copyright Iris contributors +# +# This file is part of Iris and is released under the BSD license. +# See LICENSE in the root of the repository for full licensing details. +"""Integration tests for the :mod:`iris.experimental.geovista` module.""" diff --git a/lib/iris/tests/integration/experimental/geovista/test_cube_to_poly.py b/lib/iris/tests/integration/experimental/geovista/test_cube_to_poly.py new file mode 100644 index 0000000000..582c216a44 --- /dev/null +++ b/lib/iris/tests/integration/experimental/geovista/test_cube_to_poly.py @@ -0,0 +1,67 @@ +# Copyright Iris contributors +# +# This file is part of Iris and is released under the BSD license. +# See LICENSE in the root of the repository for full licensing details. +"""Integration tests for the `iris.experimental.geovista.cube_to_polydata` function.""" + +import numpy as np + +from iris import load_cube +from iris.experimental.geovista import cube_to_polydata +from iris.experimental.ugrid import PARSE_UGRID_ON_LOAD +from iris.tests import get_data_path + + +def test_integration_2d(): + file_path = get_data_path( + [ + "NetCDF", + "ORCA2", + "votemper.nc", + ] + ) + + cube = load_cube(file_path, "votemper") + + polydata = cube_to_polydata(cube[0, 1, :]) + # This is a known good output, we have plotted the result and checked it. + assert polydata.GetNumberOfCells() == 26640 + assert polydata.GetNumberOfPoints() == 26969 + np.testing.assert_array_equal(cube[0, 1, :].data.flatten(), polydata.active_scalars) + + +def test_integration_1d(): + file_path = get_data_path( + [ + "NetCDF", + "global", + "xyt", + "SMALL_hires_wind_u_for_ipcc4.nc", + ] + ) + cube = load_cube(file_path) + + polydata = cube_to_polydata(cube[0, :]) + # This is a known good output, we have plotted the result and checked it. + assert polydata.GetNumberOfCells() == 51200 + assert polydata.GetNumberOfPoints() == 51681 + np.testing.assert_array_equal(cube[0, :].data.flatten(), polydata.active_scalars) + + +def test_integration_mesh(): + file_path = get_data_path( + [ + "NetCDF", + "unstructured_grid", + "lfric_ngvat_2D_72t_face_half_levels_main_conv_rain.nc", + ] + ) + + with PARSE_UGRID_ON_LOAD.context(): + cube = load_cube(file_path, "conv_rain") + + polydata = cube_to_polydata(cube[0, :]) + # This is a known good output, we have plotted the result and checked it. + assert polydata.GetNumberOfCells() == 864 + assert polydata.GetNumberOfPoints() == 866 + np.testing.assert_array_equal(polydata.active_scalars, cube[0, :].data) diff --git a/lib/iris/tests/integration/experimental/geovista/test_extract_unstructured_region.py b/lib/iris/tests/integration/experimental/geovista/test_extract_unstructured_region.py new file mode 100644 index 0000000000..47024dc1cd --- /dev/null +++ b/lib/iris/tests/integration/experimental/geovista/test_extract_unstructured_region.py @@ -0,0 +1,36 @@ +# Copyright Iris contributors +# +# This file is part of Iris and is released under the BSD license. +# See LICENSE in the root of the repository for full licensing details. +"""Integration tests for the `iris.experimental.geovista.extract_unstructured_region` function.""" + +from geovista.geodesic import BBox + +from iris import load_cube +from iris.experimental.geovista import cube_to_polydata, extract_unstructured_region +from iris.experimental.ugrid import PARSE_UGRID_ON_LOAD +from iris.tests import get_data_path + + +def test_face_region_extraction(): + file_path = get_data_path( + [ + "NetCDF", + "unstructured_grid", + "lfric_ngvat_2D_72t_face_half_levels_main_conv_rain.nc", + ] + ) + + with PARSE_UGRID_ON_LOAD.context(): + global_cube = load_cube(file_path, "conv_rain") + polydata = cube_to_polydata(global_cube[0, :]) + region = BBox(lons=[0, 70, 70, 0], lats=[-25, -25, 45, 45]) + + extracted_cube = extract_unstructured_region( + global_cube, polydata, region, preference="center" + ) + + assert extracted_cube.ndim == 2 + assert extracted_cube.shape == (72, 101) + assert global_cube.shape == (72, 864) + assert global_cube.ndim == 2 diff --git a/lib/iris/tests/unit/experimental/geovista/__init__.py b/lib/iris/tests/unit/experimental/geovista/__init__.py new file mode 100644 index 0000000000..b2024ce97d --- /dev/null +++ b/lib/iris/tests/unit/experimental/geovista/__init__.py @@ -0,0 +1,5 @@ +# Copyright Iris contributors +# +# This file is part of Iris and is released under the BSD license. +# See LICENSE in the root of the repository for full licensing details. +"""Unit tests for the :mod:`iris.experimental.geovista` module.""" diff --git a/lib/iris/tests/unit/experimental/geovista/test_cube_to_polydata.py b/lib/iris/tests/unit/experimental/geovista/test_cube_to_polydata.py new file mode 100644 index 0000000000..1394465fb4 --- /dev/null +++ b/lib/iris/tests/unit/experimental/geovista/test_cube_to_polydata.py @@ -0,0 +1,190 @@ +# Copyright Iris contributors +# +# This file is part of Iris and is released under the BSD license. +# See LICENSE in the root of the repository for full licensing details. +"""Unit tests for the `iris.experimental.geovista.cube_to_polydata` function.""" + +from unittest.mock import Mock + +from geovista import Transform +import numpy as np +import pytest + +import iris.analysis.cartography +import iris.coord_systems +from iris.experimental.geovista import cube_to_polydata +from iris.tests.stock import lat_lon_cube, sample_2d_latlons +from iris.tests.stock.mesh import sample_mesh_cube + + +@pytest.fixture() +def cube_mesh(): + return sample_mesh_cube() + + +@pytest.fixture() +def cube_1d(): + sample_1d_cube = lat_lon_cube() + for coord in sample_1d_cube.dim_coords: + coord.coord_system = None + return sample_1d_cube + + +@pytest.fixture() +def cube_2d(): + return sample_2d_latlons() + + +@pytest.fixture() +def default_cs(): + return iris.coord_systems.GeogCS( + iris.analysis.cartography.DEFAULT_SPHERICAL_EARTH_RADIUS + ) + + +class ParentClass: + MOCKED_OPERATION = NotImplemented + + @pytest.fixture() + def expected(self): + pass + + @pytest.fixture() + def operation(self): + pass + + @pytest.fixture() + def cube(self): + pass + + @pytest.fixture() + def cube_with_crs(self, default_cs, cube): + cube_crs = cube.copy() + for coord in cube_crs.coords(): + coord.coord_system = default_cs + return cube_crs + + @pytest.fixture() + def mocked_operation(self): + mocking = Mock() + setattr(Transform, self.MOCKED_OPERATION, mocking) + return mocking + + @staticmethod + def test_to_poly(expected, mocked_operation, cube): + cube_to_polydata(cube) + actual = mocked_operation.call_args.kwargs + for key, expected_value in expected.items(): + if hasattr(expected_value, "shape"): + np.testing.assert_array_equal(actual[key], expected_value) + else: + assert actual[key] == expected_value + + @staticmethod + def test_to_poly_crs(mocked_operation, default_cs, cube_with_crs): + cube_to_polydata(cube_with_crs) + actual = mocked_operation.call_args.kwargs + assert actual["crs"] == default_cs.as_cartopy_crs().proj4_init + + @staticmethod + def test_to_poly_kwargs(mocked_operation, cube): + kwargs = {"test": "test"} + cube_to_polydata(cube, **kwargs) + actual = mocked_operation.call_args.kwargs + assert actual["test"] == "test" + + +class Test2dToPoly(ParentClass): + MOCKED_OPERATION = "from_2d" + + @pytest.fixture() + def expected(self, cube_2d): + return { + "xs": cube_2d.coord(axis="X").contiguous_bounds(), + "ys": cube_2d.coord(axis="Y").contiguous_bounds(), + "data": cube_2d.data, + "name": f"{cube_2d.name()} / ({cube_2d.units})", + } + + @pytest.fixture() + def cube(self, cube_2d): + return cube_2d + + +class Test1dToPoly(ParentClass): + MOCKED_OPERATION = "from_1d" + + @pytest.fixture() + def expected(self, cube_1d): + return { + "xs": cube_1d.coord(axis="X").contiguous_bounds(), + "ys": cube_1d.coord(axis="Y").contiguous_bounds(), + "data": cube_1d.data, + "name": f"{cube_1d.name()} / ({cube_1d.units})", + } + + @pytest.fixture() + def cube(self, cube_1d): + return cube_1d + + +class TestMeshToPoly(ParentClass): + MOCKED_OPERATION = "from_unstructured" + + @pytest.fixture() + def expected(self, cube_mesh): + return { + "xs": cube_mesh.mesh.node_coords[0].points, + "ys": cube_mesh.mesh.node_coords[1].points, + "connectivity": cube_mesh.mesh.face_node_connectivity.indices_by_location(), + "data": cube_mesh.data[0], + "name": cube_mesh.name() + " / " + "(" + str(cube_mesh.units) + ")", + "start_index": 0, + } + + def test_if_1d(self, cube_mesh): + with pytest.raises( + NotImplementedError, + match=r"Cubes with a mesh must be one dimensional", + ): + cube_to_polydata(cube_mesh) + + @pytest.fixture() + def operation(self): + return "from_unstructured" + + @pytest.fixture() + def cube(self, cube_mesh): + return cube_mesh[0] + + @pytest.mark.skip(reason="Meshes do not support crs currently") + def test_to_poly_crs(self, expected, actual): + return NotImplemented + + +class TestExtras: + @pytest.fixture() + def cube_1d_2d(self, cube_2d): + my_cube = cube_2d.copy() + lat_coord = my_cube.aux_coords[0] + lat_coord_small = lat_coord[0] + lat_coord_small.bounds = None + lat_coord_small.points = np.arange(len(lat_coord_small.points)) + my_cube.remove_coord(lat_coord) + my_cube.add_aux_coord(lat_coord_small, 1) + return my_cube + + def test_not_1d_or_2d(self, cube_1d_2d): + with pytest.raises( + NotImplementedError, + match=r"Only 1D and 2D coordinates are supported", + ): + cube_to_polydata(cube_1d_2d) + + def test_no_mesh_or_2d(self, cube_1d): + cube = cube_1d[0] + with pytest.raises( + NotImplementedError, + match=r"Cube must have a mesh or have 2 dimensions", + ): + cube_to_polydata(cube) diff --git a/lib/iris/tests/unit/experimental/geovista/test_extract_unstructured_region.py b/lib/iris/tests/unit/experimental/geovista/test_extract_unstructured_region.py new file mode 100644 index 0000000000..57babfc764 --- /dev/null +++ b/lib/iris/tests/unit/experimental/geovista/test_extract_unstructured_region.py @@ -0,0 +1,153 @@ +# Copyright Iris contributors +# +# This file is part of Iris and is released under the BSD license. +# See LICENSE in the root of the repository for full licensing details. +"""Unit tests for the `iris.experimental.geovista.extract_unstructured_region` function.""" + +from unittest.mock import MagicMock, Mock + +from geovista.common import VTK_CELL_IDS, VTK_POINT_IDS +import numpy as np +import pytest + +from iris.experimental.geovista import extract_unstructured_region +from iris.tests.stock import sample_2d_latlons +from iris.tests.stock.mesh import sample_mesh_cube + + +class TestRegionExtraction: + @pytest.fixture() + def cube_2d(self): + return sample_2d_latlons() + + @pytest.fixture(params=["face", "node"], autouse=True) + def cube_mesh(self, request): + self.cube_mesh = sample_mesh_cube(location=request.param, n_z=10) + + @pytest.fixture() + def cube_mesh_edge(self): + return sample_mesh_cube(location="edge") + + @pytest.fixture(autouse=True) + def mocked_polydata(self): + mock_polydata_scalars = { + VTK_CELL_IDS: np.arange(2), + VTK_POINT_IDS: np.arange(14), + } + polydata = MagicMock() + polydata.__getitem__.side_effect = mock_polydata_scalars.__getitem__ + polydata.GetNumberOfCells.return_value = 3 + polydata.GetNumberOfPoints.return_value = 15 + self.mocked_polydata = polydata + + @pytest.fixture(autouse=True) + def mocked_region(self): + region = Mock() + region.enclosed.return_value = self.mocked_polydata + self.mocked_region = region + + def test_called_with(self): + extract_unstructured_region( + self.cube_mesh, self.mocked_polydata, self.mocked_region + ) + self.mocked_region.enclosed.assert_called_with(self.mocked_polydata) + + def test_kwarg(self): + extract_unstructured_region( + self.cube_mesh, + self.mocked_polydata, + self.mocked_region, + test="test", + ) + actual = self.mocked_region.enclosed.call_args.kwargs + assert actual["test"] == "test" + + @pytest.mark.parametrize( + "transpose_cube", [True, False], ids=["Transposed", "Not Transposed"] + ) + def test_indices(self, transpose_cube): + if transpose_cube: + self.cube_mesh.transpose() + extracted_region = extract_unstructured_region( + self.cube_mesh, self.mocked_polydata, self.mocked_region + ) + if self.cube_mesh.location == "face": + expected_length = len(self.mocked_polydata[VTK_CELL_IDS]) + else: + assert self.cube_mesh.location == "node" + expected_length = len(self.mocked_polydata[VTK_POINT_IDS]) + mesh_dim = self.cube_mesh.mesh_dim() + assert extracted_region.shape[mesh_dim] == expected_length + + def test_empty_indices(self): + mock_polydata_scalars = { + VTK_CELL_IDS: np.arange(0), + VTK_POINT_IDS: np.arange(0), + } + self.mocked_polydata.__getitem__.side_effect = mock_polydata_scalars.__getitem__ + with pytest.raises( + IndexError, match="No part of `polydata` falls within `region`." + ): + extract_unstructured_region( + self.cube_mesh, self.mocked_polydata, self.mocked_region + ) + + def test_recreate_mesh(self): + extracted_region = extract_unstructured_region( + self.cube_mesh, self.mocked_polydata, self.mocked_region + ) + if self.cube_mesh.location == "face": + assert extracted_region.mesh is not None + else: + assert extracted_region.mesh is None + + def test_new_mesh_coords(self): + extracted_region = extract_unstructured_region( + self.cube_mesh, self.mocked_polydata, self.mocked_region + ) + if self.cube_mesh.location == "face": + mesh_coords = extracted_region.coords(mesh_coords=True) + np.testing.assert_array_equal( + mesh_coords[0].bounds, + [[1200, 1201, 1202, 1203], [1204, 1205, 1206, 1207]], + ) + np.testing.assert_array_equal(mesh_coords[0].points, [3200, 3201]) + np.testing.assert_array_equal( + mesh_coords[1].bounds, + [[1100, 1101, 1102, 1103], [1104, 1105, 1106, 1107]], + ) + np.testing.assert_array_equal(mesh_coords[1].points, [3100, 3101]) + + def test_no_mesh(self, cube_2d): + cube = cube_2d + with pytest.raises(ValueError, match="Cube must have a mesh"): + extract_unstructured_region(cube, self.mocked_polydata, self.mocked_region) + + def test_edge_location(self, cube_mesh_edge): + with pytest.raises( + NotImplementedError, + match=f"cube.location must be `face` or `node`." + f" Found: {cube_mesh_edge.location}.", + ): + extract_unstructured_region( + cube_mesh_edge, self.mocked_polydata, self.mocked_region + ) + + def test_cube_and_poly_shapes_mismatch(self): + self.mocked_polydata.GetNumberOfCells.return_value = 4 + self.mocked_polydata.GetNumberOfPoints.return_value = 16 + polydata_length = () + if self.cube_mesh.location == "face": + polydata_length = self.mocked_polydata.GetNumberOfCells() + elif self.cube_mesh.location == "node": + polydata_length = self.mocked_polydata.GetNumberOfPoints() + with pytest.raises( + ValueError, + match=f"The mesh on the cube and the polydata" + f"must have the same shape." + f" Found Mesh: {self.cube_mesh.shape[self.cube_mesh.mesh_dim()]}," + f" Polydata: {polydata_length}.", + ): + extract_unstructured_region( + self.cube_mesh, self.mocked_polydata, self.mocked_region + ) diff --git a/requirements/locks/py310-linux-64.lock 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dependencies: # Optional dependencies. - esmpy >=7.0 + - geovista - graphviz - iris-sample-data >=2.4.0 - mo_pack