unstructured grid datasets

Author: dbochkov-flexcompute

CHANGELOG.md

@@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Added support for two-photon absorption via `TwoPhotonAbsorption` class. Added `KerrNonlinearity` that implements Kerr effect without third-harmonic generation.
 - Can create `PoleResidue` from LO-TO form via `PoleResidue.from_lo_to`.
+- Added `TriangularGridDataset` and `TehrahedralGridDataset` for storing and manipulating unstructured data.
 - Support for an anisotropic medium containing PEC components.
 - `SimulationData.mnt_data_from_file()` method to load only a single monitor data object from a simulation data `.hdf5` file.
 - `_hash_self` to base model, uses `hashlib` to hash a Tidy3D component the same way every session.

MANIFEST.in

@@ -8,4 +8,5 @@ include requirements/gdspy.txt
 include requirements/gdstk.txt
 include requirements/dev.txt
 include requirements/trimesh.txt
+include requirements/vtk.txt
 include tidy3d/web/cacert.pem

requirements/dev.txt

@@ -5,6 +5,7 @@
 -r gdspy.txt
 -r jax.txt
 -r trimesh.txt
+-r vtk.txt
 
 # required for development
 pre-commit

requirements/vtk.txt

@@ -0,0 +1,4 @@
+# vtk
+
+vtk
+

setup.py

@@ -33,6 +33,7 @@ def read_requirements(req_file: str):
 gdstk_required = read_requirements("requirements/gdstk.txt")
 gdspy_required = read_requirements("requirements/gdspy.txt")
 trimesh_required = read_requirements("requirements/trimesh.txt")
+vtk_required = read_requirements("requirements/vtk.txt")
 core_required = read_requirements("requirements/core.txt")
 core_required += basic_required + web_required
 dev_required = read_requirements("requirements/dev.txt")
@@ -72,6 +73,7 @@ def create_config_folder():
         "gdspy": gdspy_required,
         "gdstk": gdstk_required,
         "trimesh": trimesh_required,
+        "vtk": vtk_required,
     },
     entry_points={
         "console_scripts": [

test_local.sh

@@ -6,4 +6,7 @@ ruff check tidy3d
 
 pytest -rA tests/
 
+# test no vtk available (must be done separately from other tests to reload tidy3d from scratch)
+pytest -rA tests/test_data/_test_datasets_no_vtk.py
+
 pytest --doctest-modules tidy3d/components

tests/sims/simulation_2_5_0rc3.json

@@ -1011,14 +1011,14 @@
                 },
                 "transform": [
                     [
-                        0.9659258262890684,
-                        -0.2588190451025208,
+                        0.9659258262890683,
+                        -0.25881904510252074,
                         0.0,
                         0.0
                     ],
                     [
-                        0.2588190451025208,
-                        0.9659258262890684,
+                        0.25881904510252074,
+                        0.9659258262890683,
                         0.0,
                         0.0
                     ],
@@ -1506,7 +1506,7 @@
                 1,
                 1
             ],
-            "colocate": 1,
+            "colocate": true,
             "freqs": [
                 200000000000000.0,
                 250000000000000.0
@@ -1538,7 +1538,7 @@
                 1,
                 1
             ],
-            "colocate": 1,
+            "colocate": true,
             "start": 0.0,
             "stop": null,
             "interval": 1,
@@ -1687,7 +1687,7 @@
                 1,
                 1
             ],
-            "colocate": 1,
+            "colocate": true,
             "freqs": [
                 250000000000000.0,
                 300000000000000.0
@@ -1832,7 +1832,7 @@
                 1,
                 1
             ],
-            "colocate": 1,
+            "colocate": true,
             "freqs": [
                 250000000000000.0,
                 300000000000000.0
@@ -1884,7 +1884,7 @@
                 1,
                 1
             ],
-            "colocate": 1,
+            "colocate": true,
             "freqs": [
                 250000000000000.0,
                 300000000000000.0
@@ -1933,7 +1933,7 @@
                 1,
                 1
             ],
-            "colocate": 1,
+            "colocate": true,
             "freqs": [
                 250000000000000.0,
                 300000000000000.0

tests/test_components/test_heat.py

@@ -25,6 +25,7 @@
 from tidy3d import HeatSimulationData
 from tidy3d import TemperatureMonitor
 from tidy3d import TemperatureData
+from tidy3d.exceptions import DataError
 
 from ..utils import STL_GEO, assert_log_level, log_capture
 
@@ -103,12 +104,17 @@ def test_heat_bcs():
         _ = ConvectionBC(ambient_temperature=400, transfer_coeff=-0.2)
 
 
-def make_heat_mnt():
-    return TemperatureMonitor(size=(1, 2, 3), name="test")
+def make_heat_mnts():
+    temp_mnt1 = TemperatureMonitor(size=(1, 2, 3), name="test")
+    temp_mnt2 = TemperatureMonitor(size=(1, 2, 3), name="tet", unstructured=True)
+    temp_mnt3 = TemperatureMonitor(size=(1, 0, 3), name="tri", unstructured=True, conformal=True)
+    temp_mnt4 = TemperatureMonitor(size=(1, 0, 3), name="empty", unstructured=True, conformal=False)
+
+    return (temp_mnt1, temp_mnt2, temp_mnt3, temp_mnt4)
 
 
 def test_heat_mnt():
-    temp_mnt = make_heat_mnt()
+    temp_mnt, _, _, _ = make_heat_mnts()
 
     with pytest.raises(pd.ValidationError):
         _ = temp_mnt.updated_copy(name=None)
@@ -118,21 +124,75 @@ def test_heat_mnt():
 
 
 def make_heat_mnt_data():
-    temp_mnt = make_heat_mnt()
+    temp_mnt1, temp_mnt2, temp_mnt3, temp_mnt4 = make_heat_mnts()
 
     nx, ny, nz = 9, 6, 5
-    x = np.linspace(-1, 1, nx)
-    y = np.linspace(-2, 2, ny)
-    z = np.linspace(-3, 3, nz)
+    x = np.linspace(0, 1, nx)
+    y = np.linspace(0, 2, ny)
+    z = np.linspace(0, 3, nz)
     T = np.random.default_rng().uniform(300, 350, (nx, ny, nz))
     coords = dict(x=x, y=y, z=z)
     temperature_field = td.SpatialDataArray(T, coords=coords)
 
-    return TemperatureData(monitor=temp_mnt, temperature=temperature_field)
+    mnt_data1 = TemperatureData(monitor=temp_mnt1, temperature=temperature_field)
+
+    tet_grid_points = td.PointDataArray(
+        [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [1.0, 1.0, 0.0], [0.0, 0.0, 1.0]],
+        dims=("index", "axis"),
+    )
+
+    tet_grid_cells = td.CellDataArray(
+        [[0, 1, 2, 4], [1, 2, 3, 4]],
+        dims=("cell_index", "vertex_index"),
+    )
+
+    tet_grid_values = td.IndexedDataArray(
+        [1.0, 2.0, 3.0, 4.0, 5.0],
+        dims=("index"),
+        name="T",
+    )
+
+    tet_grid = td.TetrahedralGridDataset(
+        points=tet_grid_points,
+        cells=tet_grid_cells,
+        values=tet_grid_values,
+    )
+
+    mnt_data2 = TemperatureData(monitor=temp_mnt2, temperature=tet_grid)
+
+    tri_grid_points = td.PointDataArray(
+        [[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [1.0, 1.0]],
+        dims=("index", "axis"),
+    )
+
+    tri_grid_cells = td.CellDataArray(
+        [[0, 1, 2], [1, 2, 3]],
+        dims=("cell_index", "vertex_index"),
+    )
+
+    tri_grid_values = td.IndexedDataArray(
+        [1.0, 2.0, 3.0, 4.0],
+        dims=("index"),
+        name="T",
+    )
+
+    tri_grid = td.TriangularGridDataset(
+        normal_axis=1,
+        normal_pos=0,
+        points=tri_grid_points,
+        cells=tri_grid_cells,
+        values=tri_grid_values,
+    )
+
+    mnt_data3 = TemperatureData(monitor=temp_mnt3, temperature=tri_grid)
+
+    mnt_data4 = TemperatureData(monitor=temp_mnt4, temperature=None)
+
+    return (mnt_data1, mnt_data2, mnt_data3, mnt_data4)
 
 
 def test_heat_mnt_data():
-    _ = make_heat_mnt_data
+    _ = make_heat_mnt_data()
 
 
 def make_uniform_grid_spec():
@@ -192,7 +252,7 @@ def make_heat_sim():
 
     grid_spec = make_uniform_grid_spec()
 
-    temp_mnt = make_heat_mnt()
+    temp_mnts = make_heat_mnts()
 
     heat_sim = HeatSimulation(
         medium=fluid_medium,
@@ -202,7 +262,7 @@ def make_heat_sim():
         boundary_spec=[pl1, pl2, pl3, pl4, pl5],
         grid_spec=grid_spec,
         sources=[heat_source],
-        monitors=[temp_mnt],
+        monitors=temp_mnts,
     )
 
     return heat_sim
@@ -253,7 +313,7 @@ def test_heat_sim():
     with pytest.raises(pd.ValidationError):
         _ = heat_sim.updated_copy(center=(0, 0, 0), size=(1, 0, 0))
 
-    temp_mnt = make_heat_mnt()
+    temp_mnt = heat_sim.monitors[0]
 
     with pytest.raises(pd.ValidationError):
         heat_sim.updated_copy(monitors=[temp_mnt, temp_mnt])
@@ -337,7 +397,7 @@ def make_heat_sim_data():
 
     heat_sim_data = HeatSimulationData(
         simulation=heat_sim,
-        data=[temp_data],
+        data=temp_data,
     )
 
     return heat_sim_data
@@ -346,15 +406,23 @@ def make_heat_sim_data():
 def test_sim_data():
     heat_sim_data = make_heat_sim_data()
     _ = heat_sim_data.plot_field("test", z=0)
+    _ = heat_sim_data.plot_field("tri")
+    _ = heat_sim_data.plot_field("tet", y=0.5)
     plt.close()
 
+    with pytest.raises(DataError):
+        _ = heat_sim_data.plot_field("empty")
+
+    with pytest.raises(DataError):
+        _ = heat_sim_data.plot_field("test")
+
     with pytest.raises(KeyError):
         _ = heat_sim_data.plot_field("test3", x=0)
 
     with pytest.raises(pd.ValidationError):
         _ = heat_sim_data.updated_copy(data=[heat_sim_data.data[0]] * 2)
 
-    temp_mnt = make_heat_mnt()
+    temp_mnt = TemperatureMonitor(size=(1, 2, 3), name="test")
     temp_mnt = temp_mnt.updated_copy(name="test2")
 
     sim = heat_sim_data.simulation.updated_copy(monitors=[temp_mnt])

tests/test_data/_test_datasets_no_vtk.py

@@ -0,0 +1,37 @@
+"""Tests tidy3d/components/data/dataset.py"""
+import pytest
+import builtins
+from .test_datasets import test_triangular_dataset as _test_triangular_dataset
+from .test_datasets import test_tetrahedral_dataset as _test_tetrahedral_dataset
+
+
+@pytest.fixture
+def hide_vtk(monkeypatch, request):
+    import_orig = builtins.__import__
+
+    def mocked_import(name, *args, **kwargs):
+        if name in ["vtk", "vtkmodules.vtkCommonCore"]:
+            raise ImportError()
+        return import_orig(name, *args, **kwargs)
+
+    monkeypatch.setattr(builtins, "__import__", mocked_import)
+
+
+@pytest.mark.usefixtures("hide_vtk")
+def test_triangular_dataset_no_vtk(tmp_path):
+    _test_triangular_dataset(tmp_path, "test_name")
+
+    # double check that vtk was not imported
+    from tidy3d.components.types import vtk
+
+    assert vtk is None
+
+
+@pytest.mark.usefixtures("hide_vtk")
+def test_tetrahedral_dataset_no_vtk(tmp_path):
+    _test_tetrahedral_dataset(tmp_path, "test_name")
+
+    # double check that vtk was not imported
+    from tidy3d.components.types import vtk
+
+    assert vtk is None

tests/test_data/test_data_arrays.py

@@ -1,8 +1,10 @@
 """Tests tidy3d/components/data/data_array.py"""
+import pytest
 import numpy as np
 from typing import Tuple, List
 
 import tidy3d as td
+from tidy3d.exceptions import DataError
 
 np.random.seed(4)
 
@@ -277,3 +279,52 @@ def test_charge_data_array():
     n = [0, 1e-12, 2e-12]
     p = [0, 3e-12, 4e-12]
     _ = td.ChargeDataArray((1 + 1j) * np.random.random((3, 3)), coords=dict(n=n, p=p))
+
+
+def test_point_data_array():
+    _ = td.PointDataArray(
+        np.random.rand(2, 3),
+        coords=dict(index=np.arange(2), axis=np.arange(3)),
+    )
+
+
+def test_cell_data_array():
+    _ = td.CellDataArray(
+        [[0, 1, 2], [1, 2, 3]],
+        coords=dict(cell_index=np.arange(2), vertex_index=np.arange(3)),
+    )
+
+
+def test_indexed_data_array():
+    _ = td.IndexedDataArray(
+        np.random.rand(10),
+        coords=dict(index=np.arange(10)),
+    )
+
+
+def test_spatial_data_array():
+    arr = td.SpatialDataArray(
+        [[[0, 1], [2, 3]], [[4, 5], [6, 7]]],
+        coords=dict(x=[0, 1], y=[1, 2], z=[2, 3]),
+    )
+
+    reflected = arr.reflect(axis=0, center=-0.5)
+
+    reflected_expected = td.SpatialDataArray(
+        [[[4, 5], [6, 7]], [[0, 1], [2, 3]], [[0, 1], [2, 3]], [[4, 5], [6, 7]]],
+        coords=dict(x=[-2, -1, 0, 1], y=[1, 2], z=[2, 3]),
+    )
+
+    assert reflected == reflected_expected
+
+    reflected = arr.reflect(axis=1, center=1)
+
+    reflected_expected = td.SpatialDataArray(
+        [[[2, 3], [0, 1], [2, 3]], [[6, 7], [4, 5], [6, 7]]],
+        coords=dict(x=[0, 1], y=[0, 1, 2], z=[2, 3]),
+    )
+
+    assert reflected == reflected_expected
+
+    with pytest.raises(DataError):
+        reflected = arr.reflect(axis=2, center=2.5)