scipy 1.16.2__cp314-cp314-win_arm64.whl

scipy/interpolate/tests/test_rbfinterp.py

@@ -0,0 +1,534 @@
+import pickle
+import pytest
+import numpy as np
+from numpy.linalg import LinAlgError
+from scipy._lib._array_api import xp_assert_close
+from scipy.stats.qmc import Halton
+from scipy.spatial import cKDTree  # type: ignore[attr-defined]
+from scipy.interpolate._rbfinterp import (
+    _AVAILABLE, _SCALE_INVARIANT, _NAME_TO_MIN_DEGREE, _monomial_powers,
+    RBFInterpolator
+    )
+from scipy.interpolate import _rbfinterp_pythran
+from scipy._lib._testutils import _run_concurrent_barrier
+
+
+def _vandermonde(x, degree):
+    # Returns a matrix of monomials that span polynomials with the specified
+    # degree evaluated at x.
+    powers = _monomial_powers(x.shape[1], degree)
+    return _rbfinterp_pythran._polynomial_matrix(x, powers)
+
+
+def _1d_test_function(x):
+    # Test function used in Wahba's "Spline Models for Observational Data".
+    # domain ~= (0, 3), range ~= (-1.0, 0.2)
+    x = x[:, 0]
+    y = 4.26*(np.exp(-x) - 4*np.exp(-2*x) + 3*np.exp(-3*x))
+    return y
+
+
+def _2d_test_function(x):
+    # Franke's test function.
+    # domain ~= (0, 1) X (0, 1), range ~= (0.0, 1.2)
+    x1, x2 = x[:, 0], x[:, 1]
+    term1 = 0.75 * np.exp(-(9*x1-2)**2/4 - (9*x2-2)**2/4)
+    term2 = 0.75 * np.exp(-(9*x1+1)**2/49 - (9*x2+1)/10)
+    term3 = 0.5 * np.exp(-(9*x1-7)**2/4 - (9*x2-3)**2/4)
+    term4 = -0.2 * np.exp(-(9*x1-4)**2 - (9*x2-7)**2)
+    y = term1 + term2 + term3 + term4
+    return y
+
+
+def _is_conditionally_positive_definite(kernel, m):
+    # Tests whether the kernel is conditionally positive definite of order m.
+    # See chapter 7 of Fasshauer's "Meshfree Approximation Methods with
+    # MATLAB".
+    nx = 10
+    ntests = 100
+    for ndim in [1, 2, 3, 4, 5]:
+        # Generate sample points with a Halton sequence to avoid samples that
+        # are too close to each other, which can make the matrix singular.
+        seq = Halton(ndim, scramble=False, seed=np.random.RandomState())
+        for _ in range(ntests):
+            x = 2*seq.random(nx) - 1
+            A = _rbfinterp_pythran._kernel_matrix(x, kernel)
+            P = _vandermonde(x, m - 1)
+            Q, R = np.linalg.qr(P, mode='complete')
+            # Q2 forms a basis spanning the space where P.T.dot(x) = 0. Project
+            # A onto this space, and then see if it is positive definite using
+            # the Cholesky decomposition. If not, then the kernel is not c.p.d.
+            # of order m.
+            Q2 = Q[:, P.shape[1]:]
+            B = Q2.T.dot(A).dot(Q2)
+            try:
+                np.linalg.cholesky(B)
+            except np.linalg.LinAlgError:
+                return False
+
+    return True
+
+
+# Sorting the parametrize arguments is necessary to avoid a parallelization
+# issue described here: https://github.com/pytest-dev/pytest-xdist/issues/432.
+@pytest.mark.parametrize('kernel', sorted(_AVAILABLE))
+def test_conditionally_positive_definite(kernel):
+    # Test if each kernel in _AVAILABLE is conditionally positive definite of
+    # order m, where m comes from _NAME_TO_MIN_DEGREE. This is a necessary
+    # condition for the smoothed RBF interpolant to be well-posed in general.
+    m = _NAME_TO_MIN_DEGREE.get(kernel, -1) + 1
+    assert _is_conditionally_positive_definite(kernel, m)
+
+
+class _TestRBFInterpolator:
+    @pytest.mark.parametrize('kernel', sorted(_SCALE_INVARIANT))
+    def test_scale_invariance_1d(self, kernel):
+        # Verify that the functions in _SCALE_INVARIANT are insensitive to the
+        # shape parameter (when smoothing == 0) in 1d.
+        seq = Halton(1, scramble=False, seed=np.random.RandomState())
+        x = 3*seq.random(50)
+        y = _1d_test_function(x)
+        xitp = 3*seq.random(50)
+        yitp1 = self.build(x, y, epsilon=1.0, kernel=kernel)(xitp)
+        yitp2 = self.build(x, y, epsilon=2.0, kernel=kernel)(xitp)
+        xp_assert_close(yitp1, yitp2, atol=1e-8)
+
+    @pytest.mark.parametrize('kernel', sorted(_SCALE_INVARIANT))
+    def test_scale_invariance_2d(self, kernel):
+        # Verify that the functions in _SCALE_INVARIANT are insensitive to the
+        # shape parameter (when smoothing == 0) in 2d.
+        seq = Halton(2, scramble=False, seed=np.random.RandomState())
+        x = seq.random(100)
+        y = _2d_test_function(x)
+        xitp = seq.random(100)
+        yitp1 = self.build(x, y, epsilon=1.0, kernel=kernel)(xitp)
+        yitp2 = self.build(x, y, epsilon=2.0, kernel=kernel)(xitp)
+        xp_assert_close(yitp1, yitp2, atol=1e-8)
+
+    @pytest.mark.parametrize('kernel', sorted(_AVAILABLE))
+    def test_extreme_domains(self, kernel):
+        # Make sure the interpolant remains numerically stable for very
+        # large/small domains.
+        seq = Halton(2, scramble=False, seed=np.random.RandomState())
+        scale = 1e50
+        shift = 1e55
+
+        x = seq.random(100)
+        y = _2d_test_function(x)
+        xitp = seq.random(100)
+
+        if kernel in _SCALE_INVARIANT:
+            yitp1 = self.build(x, y, kernel=kernel)(xitp)
+            yitp2 = self.build(
+                x*scale + shift, y,
+                kernel=kernel
+                )(xitp*scale + shift)
+        else:
+            yitp1 = self.build(x, y, epsilon=5.0, kernel=kernel)(xitp)
+            yitp2 = self.build(
+                x*scale + shift, y,
+                epsilon=5.0/scale,
+                kernel=kernel
+                )(xitp*scale + shift)
+
+        xp_assert_close(yitp1, yitp2, atol=1e-8)
+
+    def test_polynomial_reproduction(self):
+        # If the observed data comes from a polynomial, then the interpolant
+        # should be able to reproduce the polynomial exactly, provided that
+        # `degree` is sufficiently high.
+        rng = np.random.RandomState(0)
+        seq = Halton(2, scramble=False, seed=rng)
+        degree = 3
+
+        x = seq.random(50)
+        xitp = seq.random(50)
+
+        P = _vandermonde(x, degree)
+        Pitp = _vandermonde(xitp, degree)
+
+        poly_coeffs = rng.normal(0.0, 1.0, P.shape[1])
+
+        y = P.dot(poly_coeffs)
+        yitp1 = Pitp.dot(poly_coeffs)
+        yitp2 = self.build(x, y, degree=degree)(xitp)
+
+        xp_assert_close(yitp1, yitp2, atol=1e-8)
+
+    @pytest.mark.slow
+    def test_chunking(self, monkeypatch):
+        # If the observed data comes from a polynomial, then the interpolant
+        # should be able to reproduce the polynomial exactly, provided that
+        # `degree` is sufficiently high.
+        rng = np.random.RandomState(0)
+        seq = Halton(2, scramble=False, seed=rng)
+        degree = 3
+
+        largeN = 1000 + 33
+        # this is large to check that chunking of the RBFInterpolator is tested
+        x = seq.random(50)
+        xitp = seq.random(largeN)
+
+        P = _vandermonde(x, degree)
+        Pitp = _vandermonde(xitp, degree)
+
+        poly_coeffs = rng.normal(0.0, 1.0, P.shape[1])
+
+        y = P.dot(poly_coeffs)
+        yitp1 = Pitp.dot(poly_coeffs)
+        interp = self.build(x, y, degree=degree)
+        ce_real = interp._chunk_evaluator
+
+        def _chunk_evaluator(*args, **kwargs):
+            kwargs.update(memory_budget=100)
+            return ce_real(*args, **kwargs)
+
+        monkeypatch.setattr(interp, '_chunk_evaluator', _chunk_evaluator)
+        yitp2 = interp(xitp)
+        xp_assert_close(yitp1, yitp2, atol=1e-8)
+
+    def test_vector_data(self):
+        # Make sure interpolating a vector field is the same as interpolating
+        # each component separately.
+        seq = Halton(2, scramble=False, seed=np.random.RandomState())
+
+        x = seq.random(100)
+        xitp = seq.random(100)
+
+        y = np.array([_2d_test_function(x),
+                      _2d_test_function(x[:, ::-1])]).T
+
+        yitp1 = self.build(x, y)(xitp)
+        yitp2 = self.build(x, y[:, 0])(xitp)
+        yitp3 = self.build(x, y[:, 1])(xitp)
+
+        xp_assert_close(yitp1[:, 0], yitp2)
+        xp_assert_close(yitp1[:, 1], yitp3)
+
+    def test_complex_data(self):
+        # Interpolating complex input should be the same as interpolating the
+        # real and complex components.
+        seq = Halton(2, scramble=False, seed=np.random.RandomState())
+
+        x = seq.random(100)
+        xitp = seq.random(100)
+
+        y = _2d_test_function(x) + 1j*_2d_test_function(x[:, ::-1])
+
+        yitp1 = self.build(x, y)(xitp)
+        yitp2 = self.build(x, y.real)(xitp)
+        yitp3 = self.build(x, y.imag)(xitp)
+
+        xp_assert_close(yitp1.real, yitp2)
+        xp_assert_close(yitp1.imag, yitp3)
+
+    @pytest.mark.parametrize('kernel', sorted(_AVAILABLE))
+    def test_interpolation_misfit_1d(self, kernel):
+        # Make sure that each kernel, with its default `degree` and an
+        # appropriate `epsilon`, does a good job at interpolation in 1d.
+        seq = Halton(1, scramble=False, seed=np.random.RandomState())
+
+        x = 3*seq.random(50)
+        xitp = 3*seq.random(50)
+
+        y = _1d_test_function(x)
+        ytrue = _1d_test_function(xitp)
+        yitp = self.build(x, y, epsilon=5.0, kernel=kernel)(xitp)
+
+        mse = np.mean((yitp - ytrue)**2)
+        assert mse < 1.0e-4
+
+    @pytest.mark.parametrize('kernel', sorted(_AVAILABLE))
+    def test_interpolation_misfit_2d(self, kernel):
+        # Make sure that each kernel, with its default `degree` and an
+        # appropriate `epsilon`, does a good job at interpolation in 2d.
+        seq = Halton(2, scramble=False, seed=np.random.RandomState())
+
+        x = seq.random(100)
+        xitp = seq.random(100)
+
+        y = _2d_test_function(x)
+        ytrue = _2d_test_function(xitp)
+        yitp = self.build(x, y, epsilon=5.0, kernel=kernel)(xitp)
+
+        mse = np.mean((yitp - ytrue)**2)
+        assert mse < 2.0e-4
+
+    @pytest.mark.parametrize('kernel', sorted(_AVAILABLE))
+    def test_smoothing_misfit(self, kernel):
+        # Make sure we can find a smoothing parameter for each kernel that
+        # removes a sufficient amount of noise.
+        rng = np.random.RandomState(0)
+        seq = Halton(1, scramble=False, seed=rng)
+
+        noise = 0.2
+        rmse_tol = 0.1
+        smoothing_range = 10**np.linspace(-4, 1, 20)
+
+        x = 3*seq.random(100)
+        y = _1d_test_function(x) + rng.normal(0.0, noise, (100,))
+        ytrue = _1d_test_function(x)
+        rmse_within_tol = False
+        for smoothing in smoothing_range:
+            ysmooth = self.build(
+                x, y,
+                epsilon=1.0,
+                smoothing=smoothing,
+                kernel=kernel)(x)
+            rmse = np.sqrt(np.mean((ysmooth - ytrue)**2))
+            if rmse < rmse_tol:
+                rmse_within_tol = True
+                break
+
+        assert rmse_within_tol
+
+    def test_array_smoothing(self):
+        # Test using an array for `smoothing` to give less weight to a known
+        # outlier.
+        rng = np.random.RandomState(0)
+        seq = Halton(1, scramble=False, seed=rng)
+        degree = 2
+
+        x = seq.random(50)
+        P = _vandermonde(x, degree)
+        poly_coeffs = rng.normal(0.0, 1.0, P.shape[1])
+        y = P.dot(poly_coeffs)
+        y_with_outlier = np.copy(y)
+        y_with_outlier[10] += 1.0
+        smoothing = np.zeros((50,))
+        smoothing[10] = 1000.0
+        yitp = self.build(x, y_with_outlier, smoothing=smoothing)(x)
+        # Should be able to reproduce the uncorrupted data almost exactly.
+        xp_assert_close(yitp, y, atol=1e-4)
+
+    def test_inconsistent_x_dimensions_error(self):
+        # ValueError should be raised if the observation points and evaluation
+        # points have a different number of dimensions.
+        y = Halton(2, scramble=False, seed=np.random.RandomState()).random(10)
+        d = _2d_test_function(y)
+        x = Halton(1, scramble=False, seed=np.random.RandomState()).random(10)
+        match = 'Expected the second axis of `x`'
+        with pytest.raises(ValueError, match=match):
+            self.build(y, d)(x)
+
+    def test_inconsistent_d_length_error(self):
+        y = np.linspace(0, 1, 5)[:, None]
+        d = np.zeros(1)
+        match = 'Expected the first axis of `d`'
+        with pytest.raises(ValueError, match=match):
+            self.build(y, d)
+
+    def test_y_not_2d_error(self):
+        y = np.linspace(0, 1, 5)
+        d = np.zeros(5)
+        match = '`y` must be a 2-dimensional array.'
+        with pytest.raises(ValueError, match=match):
+            self.build(y, d)
+
+    def test_inconsistent_smoothing_length_error(self):
+        y = np.linspace(0, 1, 5)[:, None]
+        d = np.zeros(5)
+        smoothing = np.ones(1)
+        match = 'Expected `smoothing` to be'
+        with pytest.raises(ValueError, match=match):
+            self.build(y, d, smoothing=smoothing)
+
+    def test_invalid_kernel_name_error(self):
+        y = np.linspace(0, 1, 5)[:, None]
+        d = np.zeros(5)
+        match = '`kernel` must be one of'
+        with pytest.raises(ValueError, match=match):
+            self.build(y, d, kernel='test')
+
+    def test_epsilon_not_specified_error(self):
+        y = np.linspace(0, 1, 5)[:, None]
+        d = np.zeros(5)
+        for kernel in _AVAILABLE:
+            if kernel in _SCALE_INVARIANT:
+                continue
+
+            match = '`epsilon` must be specified'
+            with pytest.raises(ValueError, match=match):
+                self.build(y, d, kernel=kernel)
+
+    def test_x_not_2d_error(self):
+        y = np.linspace(0, 1, 5)[:, None]
+        x = np.linspace(0, 1, 5)
+        d = np.zeros(5)
+        match = '`x` must be a 2-dimensional array.'
+        with pytest.raises(ValueError, match=match):
+            self.build(y, d)(x)
+
+    def test_not_enough_observations_error(self):
+        y = np.linspace(0, 1, 1)[:, None]
+        d = np.zeros(1)
+        match = 'At least 2 data points are required'
+        with pytest.raises(ValueError, match=match):
+            self.build(y, d, kernel='thin_plate_spline')
+
+    @pytest.mark.thread_unsafe
+    def test_degree_warning(self):
+        y = np.linspace(0, 1, 5)[:, None]
+        d = np.zeros(5)
+        for kernel, deg in _NAME_TO_MIN_DEGREE.items():
+            # Only test for kernels that its minimum degree is not 0.
+            if deg >= 1:
+                match = f'`degree` should not be below {deg}'
+                with pytest.warns(Warning, match=match):
+                    self.build(y, d, epsilon=1.0, kernel=kernel, degree=deg-1)
+
+    def test_minus_one_degree(self):
+        # Make sure a degree of -1 is accepted without any warning.
+        y = np.linspace(0, 1, 5)[:, None]
+        d = np.zeros(5)
+        for kernel, _ in _NAME_TO_MIN_DEGREE.items():
+            self.build(y, d, epsilon=1.0, kernel=kernel, degree=-1)
+
+    def test_rank_error(self):
+        # An error should be raised when `kernel` is "thin_plate_spline" and
+        # observations are 2-D and collinear.
+        y = np.array([[2.0, 0.0], [1.0, 0.0], [0.0, 0.0]])
+        d = np.array([0.0, 0.0, 0.0])
+        match = 'does not have full column rank'
+        with pytest.raises(LinAlgError, match=match):
+            self.build(y, d, kernel='thin_plate_spline')(y)
+
+    def test_single_point(self):
+        # Make sure interpolation still works with only one point (in 1, 2, and
+        # 3 dimensions).
+        for dim in [1, 2, 3]:
+            y = np.zeros((1, dim))
+            d = np.ones((1,))
+            f = self.build(y, d, kernel='linear')(y)
+            xp_assert_close(d, f)
+
+    def test_pickleable(self):
+        # Make sure we can pickle and unpickle the interpolant without any
+        # changes in the behavior.
+        seq = Halton(1, scramble=False, seed=np.random.RandomState(2305982309))
+
+        x = 3*seq.random(50)
+        xitp = 3*seq.random(50)
+
+        y = _1d_test_function(x)
+
+        interp = self.build(x, y)
+
+        yitp1 = interp(xitp)
+        yitp2 = pickle.loads(pickle.dumps(interp))(xitp)
+
+        xp_assert_close(yitp1, yitp2, atol=1e-16)
+
+
+class TestRBFInterpolatorNeighborsNone(_TestRBFInterpolator):
+    def build(self, *args, **kwargs):
+        return RBFInterpolator(*args, **kwargs)
+
+    def test_smoothing_limit_1d(self):
+        # For large smoothing parameters, the interpolant should approach a
+        # least squares fit of a polynomial with the specified degree.
+        seq = Halton(1, scramble=False, seed=np.random.RandomState())
+
+        degree = 3
+        smoothing = 1e8
+
+        x = 3*seq.random(50)
+        xitp = 3*seq.random(50)
+
+        y = _1d_test_function(x)
+
+        yitp1 = self.build(
+            x, y,
+            degree=degree,
+            smoothing=smoothing
+            )(xitp)
+
+        P = _vandermonde(x, degree)
+        Pitp = _vandermonde(xitp, degree)
+        yitp2 = Pitp.dot(np.linalg.lstsq(P, y, rcond=None)[0])
+
+        xp_assert_close(yitp1, yitp2, atol=1e-8)
+
+    def test_smoothing_limit_2d(self):
+        # For large smoothing parameters, the interpolant should approach a
+        # least squares fit of a polynomial with the specified degree.
+        seq = Halton(2, scramble=False, seed=np.random.RandomState())
+
+        degree = 3
+        smoothing = 1e8
+
+        x = seq.random(100)
+        xitp = seq.random(100)
+
+        y = _2d_test_function(x)
+
+        yitp1 = self.build(
+            x, y,
+            degree=degree,
+            smoothing=smoothing
+            )(xitp)
+
+        P = _vandermonde(x, degree)
+        Pitp = _vandermonde(xitp, degree)
+        yitp2 = Pitp.dot(np.linalg.lstsq(P, y, rcond=None)[0])
+
+        xp_assert_close(yitp1, yitp2, atol=1e-8)
+
+
+class TestRBFInterpolatorNeighbors20(_TestRBFInterpolator):
+    # RBFInterpolator using 20 nearest neighbors.
+    def build(self, *args, **kwargs):
+        return RBFInterpolator(*args, **kwargs, neighbors=20)
+
+    def test_equivalent_to_rbf_interpolator(self):
+        seq = Halton(2, scramble=False, seed=np.random.RandomState())
+
+        x = seq.random(100)
+        xitp = seq.random(100)
+
+        y = _2d_test_function(x)
+
+        yitp1 = self.build(x, y)(xitp)
+
+        yitp2 = []
+        tree = cKDTree(x)
+        for xi in xitp:
+            _, nbr = tree.query(xi, 20)
+            yitp2.append(RBFInterpolator(x[nbr], y[nbr])(xi[None])[0])
+
+        xp_assert_close(yitp1, yitp2, atol=1e-8)
+
+    def test_concurrency(self):
+        # Check that no segfaults appear with concurrent access to
+        # RbfInterpolator
+        seq = Halton(2, scramble=False, seed=np.random.RandomState(0))
+        x = seq.random(100)
+        xitp = seq.random(100)
+
+        y = _2d_test_function(x)
+
+        interp = self.build(x, y)
+
+        def worker_fn(_, interp, xp):
+            interp(xp)
+
+        _run_concurrent_barrier(10, worker_fn, interp, xitp)
+
+
+class TestRBFInterpolatorNeighborsInf(TestRBFInterpolatorNeighborsNone):
+    # RBFInterpolator using neighbors=np.inf. This should give exactly the same
+    # results as neighbors=None, but it will be slower.
+    def build(self, *args, **kwargs):
+        return RBFInterpolator(*args, **kwargs, neighbors=np.inf)
+
+    def test_equivalent_to_rbf_interpolator(self):
+        seq = Halton(1, scramble=False, seed=np.random.RandomState())
+
+        x = 3*seq.random(50)
+        xitp = 3*seq.random(50)
+
+        y = _1d_test_function(x)
+        yitp1 = self.build(x, y)(xitp)
+        yitp2 = RBFInterpolator(x, y)(xitp)
+
+        xp_assert_close(yitp1, yitp2, atol=1e-8)