Merge pull request #2380 from pybamm-team/add-three-dimensional-inter…

…polation

Add three dimensional interpolation

CHANGELOG.md

@@ -1,5 +1,9 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+## Features
+
+- Added three-dimensional interpolation [#2380](https://github.com/pybamm-team/PyBaMM/pull/2380)
+
 ## Bug fixes
 
 - For simulations with events that cause the simulation to stop early, the sensitivities could be evaluated incorrectly to zero ([#2337](https://github.com/pybamm-team/PyBaMM/pull/2337))

examples/notebooks/Getting Started/Tutorial 6 - Managing simulation outputs.ipynb

@@ -436,7 +436,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3.9.13 ('python39-pybamm')",
    "language": "python",
    "name": "python3"
   },
@@ -450,7 +450,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.9.13"
   },
   "toc": {
    "base_numbering": 1,
@@ -464,6 +464,11 @@
    "toc_position": {},
    "toc_section_display": true,
    "toc_window_display": true
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "7dc94e087d5e42ea54b14035c48a0a59093d5180e7f512a1db8f70eb4b99d01e"
+   }
   }
  },
  "nbformat": 4,

examples/scripts/minimal_interp3d_example.py

@@ -0,0 +1,72 @@
+import numpy as np
+
+import pybamm
+import matplotlib.pyplot as plt
+
+
+def f(x, y, z):
+    return 2 * x**3 + 3 * y**2 - z
+
+
+x = np.linspace(1, 4, 100)
+y = np.linspace(4, 7, 105)
+z = np.linspace(7, 9, 110)
+xg, yg, zg = np.meshgrid(x, y, z, indexing="ij", sparse=True)
+data = f(xg, yg, zg)
+
+x_in = (x, y, z)
+
+model = pybamm.BaseModel()
+
+a = pybamm.Variable("a")
+b = pybamm.Variable("b")
+c = pybamm.Variable("c")
+d = pybamm.Variable("d")
+
+interp = pybamm.Interpolant(x_in, data, (a, b, c), interpolator="linear")
+
+model.rhs = {a: 3, b: 3, c: 2, d: interp}  # add to model
+model.initial_conditions = {
+    a: pybamm.Scalar(1),
+    b: pybamm.Scalar(4),
+    c: pybamm.Scalar(7),
+    d: pybamm.Scalar(0),
+}
+
+model.variables = {
+    "Something": interp,
+    "a": a,
+    "b": b,
+    "c": c,
+    "d": d,
+}
+
+# solver = pybamm.CasadiSolver()
+sim = pybamm.Simulation(model)
+
+t_eval = np.linspace(0, 1, 100)
+sim.solve(t_eval)
+
+a_eval = sim.solution["a"](t_eval)
+b_eval = sim.solution["b"](t_eval)
+c_eval = sim.solution["c"](t_eval)
+d_eval = sim.solution["d"](t_eval)
+something = sim.solution["Something"](t_eval)
+
+difference = something - f(a_eval, b_eval, c_eval)
+
+fig, ax = plt.subplots(2, 1, figsize=(10, 5), sharex=True)
+
+ax[0].plot(t_eval, f(a_eval, b_eval, c_eval), label="Original")
+ax[0].plot(t_eval, something, label="Interpolated")
+ax[0].set_ylabel("Value")
+ax[0].legend()
+
+ax[1].plot(t_eval, np.abs(f(a_eval, b_eval, c_eval) - something), label="Original")
+ax[1].set_ylabel("Difference")
+
+ax[-1].set_xlabel("Time [s]")
+for a in ax:
+    a.grid()
+
+plt.show()

pybamm/expression_tree/interpolant.py

@@ -10,14 +10,18 @@
 
 class Interpolant(pybamm.Function):
     """
-    Interpolate data in 1D.
+    Interpolate data in 1D, 2D, or 3D. Interpolation in 3D requires the input data to be
+    on a regular grid (as per scipy.interpolate.RegularGridInterpolator).
 
     Parameters
     ----------
     x : iterable of :class:`numpy.ndarray`
-        1-D array(s) of real values defining the data point coordinates.
+        The data point coordinates. If 1-D, then this is an array(s) of real values. If,
+        2D or 3D interpolation, then this is to ba a tuple of 1D arrays (one for each
+        dimension) which together define the coordinates of the points.
     y : :class:`numpy.ndarray`
-        The values of the function to interpolate at the data points.
+        The values of the function to interpolate at the data points. In 2D and 3D, this
+        should be a matrix of two and three dimensions respectively.
     children : iterable of :class:`pybamm.Symbol`
         Node(s) to use when evaluating the interpolant. Each child corresponds to an
         entry of x
@@ -26,10 +30,13 @@ class Interpolant(pybamm.Function):
         function" is given.
     interpolator : str, optional
         Which interpolator to use. Can be "linear", "cubic", or "pchip". Default is
-        "linear".
+        "linear". For 3D interpolation, only "linear" an "cubic" are currently
+        supported.
     extrapolate : bool, optional
         Whether to extrapolate for points that are outside of the parametrisation
         range, or return NaN (following default behaviour from scipy). Default is True.
+        Generally, it is best to set this to be False for 3D interpolation due to
+        the higher potential for errors in extrapolation.
 
     **Extends**: :class:`pybamm.Function`
     """
@@ -71,6 +78,26 @@ def __init__(
                     "len(x2) should equal y=shape[0], "
                     f"but x2.shape={x2.shape} and y.shape={y.shape}"
                 )
+        elif isinstance(x, (tuple, list)) and len(x) == 3:
+            x1, x2, x3 = x
+            if y.ndim != 3:
+                raise ValueError("y should be three-dimensional if len(x)=3")
+
+            if x1.shape[0] != y.shape[0]:
+                raise ValueError(
+                    "len(x1) should equal y=shape[0], "
+                    f"but x1.shape={x1.shape} and y.shape={y.shape}"
+                )
+            if x2 is not None and x2.shape[0] != y.shape[1]:
+                raise ValueError(
+                    "len(x2) should equal y=shape[1], "
+                    f"but x2.shape={x2.shape} and y.shape={y.shape}"
+                )
+            if x3 is not None and x3.shape[0] != y.shape[2]:
+                raise ValueError(
+                    "len(x3) should equal y=shape[2], "
+                    f"but x3.shape={x3.shape} and y.shape={y.shape}"
+                )
         else:
             if isinstance(x, (tuple, list)):
                 x1 = x[0]
@@ -129,6 +156,28 @@ def __init__(
                 interpolating_function = interpolate.interp2d(
                     x1, x2, y, kind=interpolator
                 )
+        elif len(x) == 3:
+            self.dimension = 3
+
+            if extrapolate:
+                fill_value = None
+            else:
+                fill_value = np.nan
+
+            possible_interpolators = ["linear", "cubic"]
+            if interpolator not in possible_interpolators:
+                raise ValueError(
+                    """interpolator should be 'linear' or 'cubic'
+                    for 3D interpolation"""
+                )
+            else:
+                interpolating_function = interpolate.RegularGridInterpolator(
+                    (x1, x2, x3),
+                    y,
+                    method=interpolator,
+                    bounds_error=False,
+                    fill_value=fill_value,
+                )
         else:
             raise ValueError("Invalid dimension of x: {0}".format(len(x)))
 
@@ -197,7 +246,48 @@ def _function_evaluate(self, evaluated_children):
             if res.ndim > 1:
                 return np.diagonal(res)[:, np.newaxis]
             else:
-                # raise ValueError("Invalid children dimension: {0}".format(res.ndim))
                 return res[:, np.newaxis]
+        elif self.dimension == 3:
+
+            # If the children are scalars, we need to add a dimension
+            shapes = []
+            for child in evaluated_children:
+                if isinstance(child, (float, int)):
+                    shapes.append(())
+                else:
+                    shapes.append(child.shape)
+            shapes = set(shapes)
+            shapes.discard(())
+
+            if len(shapes) > 1:
+                raise ValueError(
+                    "All children must have the same shape for 3D interpolation"
+                )
+
+            if len(shapes) == 0:
+                shape = (1,)
+            else:
+                shape = shapes.pop()
+            new_evaluated_children = []
+            for child in evaluated_children:
+
+                if hasattr(child, "shape") and child.shape == shape:
+                    new_evaluated_children.append(child.flatten())
+                else:
+                    new_evaluated_children.append(np.reshape(child, shape).flatten())
+
+            # return nans if there are any within the children
+            nans = np.isnan(new_evaluated_children)
+            if np.any(nans):
+                nan_children = []
+                for child, interp_range in zip(
+                    new_evaluated_children, self.function.grid
+                ):
+                    nan_children.append(np.ones_like(child) * interp_range.mean())
+                return self.function(np.transpose(nan_children)) * np.nan
+            else:
+                res = self.function(np.transpose(new_evaluated_children))
+                return res[:, np.newaxis]
+
         else:  # pragma: no cover
             raise ValueError("Invalid dimension: {0}".format(self.dimension))

pybamm/expression_tree/operations/convert_to_casadi.py

@@ -152,7 +152,7 @@ def _convert(self, symbol, t, y, y_dot, inputs):
                     return casadi.interpolant(
                         "LUT", solver, symbol.x, symbol.y.flatten()
                     )(*converted_children)
-                elif len(converted_children) == 2:
+                elif len(converted_children) in [2, 3]:
                     LUT = casadi.interpolant(
                         "LUT", solver, symbol.x, symbol.y.ravel(order="F")
                     )

tests/unit/test_expression_tree/test_interpolant.py

@@ -97,6 +97,102 @@ def test_interpolation_2_x_2d_y(self):
             interp.evaluate(y=np.array([0, 0])), 0, decimal=3
         )
 
+    def test_interpolation_3_x(self):
+        def f(x, y, z):
+            return 2 * x**3 + 3 * y**2 - z
+
+        x = np.linspace(1, 4, 11)
+        y = np.linspace(4, 7, 22)
+        z = np.linspace(7, 9, 33)
+        xg, yg, zg = np.meshgrid(x, y, z, indexing="ij", sparse=True)
+        data = f(xg, yg, zg)
+
+        var1 = pybamm.StateVector(slice(0, 1))
+        var2 = pybamm.StateVector(slice(1, 2))
+        var3 = pybamm.StateVector(slice(2, 3))
+
+        x_in = (x, y, z)
+        interp = pybamm.Interpolant(
+            x_in, data, (var1, var2, var3), interpolator="linear"
+        )
+
+        value = interp.evaluate(y=np.array([1, 5, 8]))
+        np.testing.assert_equal(value, f(1, 5, 8))
+
+        value = interp.evaluate(y=np.array([[1, 1, 1], [5, 4, 4], [8, 7, 7]]))
+        np.testing.assert_array_equal(
+            value, np.array([[f(1, 5, 8)], [f(1, 4, 7)], [f(1, 4, 7)]])
+        )
+
+        # check also works for cubic
+        interp = pybamm.Interpolant(
+            x_in, data, (var1, var2, var3), interpolator="cubic"
+        )
+        value = interp.evaluate(y=np.array([1, 5, 8]))
+        np.testing.assert_equal(value, f(1, 5, 8))
+
+        # Test raising error if data is not 3D
+        data_4d = np.zeros((11, 22, 33, 5))
+        with self.assertRaisesRegex(ValueError, "y should be three-dimensional"):
+            interp = pybamm.Interpolant(
+                x_in, data_4d, (var1, var2, var3), interpolator="linear"
+            )
+
+        # Test raising error if wrong shapes
+        with self.assertRaisesRegex(ValueError, "x1.shape"):
+            interp = pybamm.Interpolant(
+                x_in, np.zeros((12, 22, 33)), (var1, var2, var3), interpolator="linear"
+            )
+
+        with self.assertRaisesRegex(ValueError, "x2.shape"):
+            interp = pybamm.Interpolant(
+                x_in, np.zeros((11, 23, 33)), (var1, var2, var3), interpolator="linear"
+            )
+
+        with self.assertRaisesRegex(ValueError, "x3.shape"):
+            interp = pybamm.Interpolant(
+                x_in, np.zeros((11, 22, 34)), (var1, var2, var3), interpolator="linear"
+            )
+
+        # Raise error if not linear
+        with self.assertRaisesRegex(
+            ValueError, "interpolator should be 'linear' or 'cubic'"
+        ):
+            interp = pybamm.Interpolant(
+                x_in, data, (var1, var2, var3), interpolator="pchip"
+            )
+
+        # Check returns nan if extrapolate set to False
+        interp = pybamm.Interpolant(
+            x_in, data, (var1, var2, var3), interpolator="linear", extrapolate=False
+        )
+        value = interp.evaluate(y=np.array([0, 0, 0]))
+        np.testing.assert_equal(value, np.nan)
+
+        # Check testing for shape works (i.e. using nans)
+        interp = pybamm.Interpolant(
+            x_in, data, (var1, var2, var3), interpolator="cubic"
+        )
+        interp.test_shape()
+
+        # test with inconsistent children shapes
+        # (this can occur is one child is a scaler and the others
+        # are vaiables)
+        evaluated_children = [np.array([[1]]), 4, np.array([[7]])]
+        value = interp._function_evaluate(evaluated_children)
+
+        evaluated_children = [np.array([[1]]), np.ones(()) * 4, np.array([[7]])]
+        value = interp._function_evaluate(evaluated_children)
+
+        # Test evaluation fails with different child shapes
+        with self.assertRaisesRegex(ValueError, "All children must"):
+            evaluated_children = [np.array([[1, 1]]), np.ones(()) * 4, np.array([[7]])]
+            value = interp._function_evaluate(evaluated_children)
+
+        # Test runs when all children are scalsrs
+        evaluated_children = [1, 4, 7]
+        value = interp._function_evaluate(evaluated_children)
+
     def test_name(self):
         a = pybamm.Symbol("a")
         x = np.linspace(0, 1, 200)