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# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import itertools
import numpy as np
from numpy.testing import assert_almost_equal, assert_allclose
from ...tests.helper import pytest
from ..convolve import convolve, convolve_fft
from ..kernels import (
Gaussian1DKernel, Gaussian2DKernel, Box1DKernel, Box2DKernel,
Trapezoid1DKernel, TrapezoidDisk2DKernel, MexicanHat1DKernel,
Tophat2DKernel, MexicanHat2DKernel, AiryDisk2DKernel, Ring2DKernel,
CustomKernel, Model1DKernel, Model2DKernel, Kernel1D, Kernel2D)
from ..utils import KernelSizeError
from ...modeling.models import Box2D, Gaussian1D, Gaussian2D
from ...utils.exceptions import AstropyWarning, AstropyUserWarning
try:
from scipy.ndimage import filters
HAS_SCIPY = True
except ImportError:
HAS_SCIPY = False
WIDTHS_ODD = [3, 5, 7, 9]
WIDTHS_EVEN = [2, 4, 8, 16]
MODES = ['center', 'linear_interp', 'oversample', 'integrate']
KERNEL_TYPES = [Gaussian1DKernel, Gaussian2DKernel,
Box1DKernel, Box2DKernel,
Trapezoid1DKernel, TrapezoidDisk2DKernel,
MexicanHat1DKernel, Tophat2DKernel, AiryDisk2DKernel, Ring2DKernel]
NUMS = [1, 1., np.float(1.), np.float32(1.), np.float64(1.)]
# Test data
delta_pulse_1D = np.zeros(81)
delta_pulse_1D[40] = 1
delta_pulse_2D = np.zeros((81, 81))
delta_pulse_2D[40, 40] = 1
random_data_1D = np.random.rand(61)
random_data_2D = np.random.rand(61, 61)
class TestKernels(object):
"""
Test class for the built-in convolution kernels.
"""
@pytest.mark.skipif('not HAS_SCIPY')
@pytest.mark.parametrize(('width'), WIDTHS_ODD)
def test_scipy_filter_gaussian(self, width):
"""
Test GaussianKernel against SciPy ndimage gaussian filter.
"""
gauss_kernel_1D = Gaussian1DKernel(width)
gauss_kernel_1D.normalize()
gauss_kernel_2D = Gaussian2DKernel(width)
gauss_kernel_2D.normalize()
astropy_1D = convolve(delta_pulse_1D, gauss_kernel_1D, boundary='fill')
astropy_2D = convolve(delta_pulse_2D, gauss_kernel_2D, boundary='fill')
scipy_1D = filters.gaussian_filter(delta_pulse_1D, width)
scipy_2D = filters.gaussian_filter(delta_pulse_2D, width)
assert_almost_equal(astropy_1D, scipy_1D, decimal=12)
assert_almost_equal(astropy_2D, scipy_2D, decimal=12)
@pytest.mark.skipif('not HAS_SCIPY')
@pytest.mark.parametrize(('width'), WIDTHS_ODD)
def test_scipy_filter_gaussian_laplace(self, width):
"""
Test MexicanHat kernels against SciPy ndimage gaussian laplace filters.
"""
mexican_kernel_1D = MexicanHat1DKernel(width)
mexican_kernel_2D = MexicanHat2DKernel(width)
astropy_1D = convolve(delta_pulse_1D, mexican_kernel_1D, boundary='fill')
astropy_2D = convolve(delta_pulse_2D, mexican_kernel_2D, boundary='fill')
# The Laplace of Gaussian filter is an inverted Mexican Hat
# filter.
scipy_1D = -filters.gaussian_laplace(delta_pulse_1D, width)
scipy_2D = -filters.gaussian_laplace(delta_pulse_2D, width)
# There is a slight deviation in the normalization. They differ by a
# factor of ~1.0000284132604045. The reason is not known.
assert_almost_equal(astropy_1D, scipy_1D, decimal=5)
assert_almost_equal(astropy_2D, scipy_2D, decimal=5)
@pytest.mark.parametrize(('kernel_type', 'width'), list(itertools.product(KERNEL_TYPES, WIDTHS_ODD)))
def test_delta_data(self, kernel_type, width):
"""
Test smoothing of an image with a single positive pixel
"""
if kernel_type == AiryDisk2DKernel and not HAS_SCIPY:
pytest.skip("Omitting AiryDisk2DKernel, which requires SciPy")
if not kernel_type == Ring2DKernel:
kernel = kernel_type(width)
else:
kernel = kernel_type(width, width * 0.2)
if kernel.dimension == 1:
c1 = convolve_fft(delta_pulse_1D, kernel, boundary='fill')
c2 = convolve(delta_pulse_1D, kernel, boundary='fill')
assert_almost_equal(c1, c2, decimal=12)
else:
c1 = convolve_fft(delta_pulse_2D, kernel, boundary='fill')
c2 = convolve(delta_pulse_2D, kernel, boundary='fill')
assert_almost_equal(c1, c2, decimal=12)
@pytest.mark.parametrize(('kernel_type', 'width'), list(itertools.product(KERNEL_TYPES, WIDTHS_ODD)))
def test_random_data(self, kernel_type, width):
"""
Test smoothing of an image made of random noise
"""
if kernel_type == AiryDisk2DKernel and not HAS_SCIPY:
pytest.skip("Omitting AiryDisk2DKernel, which requires SciPy")
if not kernel_type == Ring2DKernel:
kernel = kernel_type(width)
else:
kernel = kernel_type(width, width * 0.2)
if kernel.dimension == 1:
c1 = convolve_fft(random_data_1D, kernel, boundary='fill')
c2 = convolve(random_data_1D, kernel, boundary='fill')
assert_almost_equal(c1, c2, decimal=12)
else:
c1 = convolve_fft(random_data_2D, kernel, boundary='fill')
c2 = convolve(random_data_2D, kernel, boundary='fill')
assert_almost_equal(c1, c2, decimal=12)
@pytest.mark.parametrize(('width'), WIDTHS_ODD)
def test_uniform_smallkernel(self, width):
"""
Test smoothing of an image with a single positive pixel
Instead of using kernel class, uses a simple, small kernel
"""
kernel = np.ones([width, width])
c2 = convolve_fft(delta_pulse_2D, kernel, boundary='fill')
c1 = convolve(delta_pulse_2D, kernel, boundary='fill')
assert_almost_equal(c1, c2, decimal=12)
@pytest.mark.parametrize(('width'), WIDTHS_ODD)
def test_smallkernel_vs_Box2DKernel(self, width):
"""
Test smoothing of an image with a single positive pixel
"""
kernel1 = np.ones([width, width]) / width ** 2
kernel2 = Box2DKernel(width)
c2 = convolve_fft(delta_pulse_2D, kernel2, boundary='fill')
c1 = convolve_fft(delta_pulse_2D, kernel1, boundary='fill')
assert_almost_equal(c1, c2, decimal=12)
def test_convolve_1D_kernels(self):
"""
Check if convolving two kernels with each other works correctly.
"""
gauss_1 = Gaussian1DKernel(3)
gauss_2 = Gaussian1DKernel(4)
test_gauss_3 = Gaussian1DKernel(5)
gauss_3 = convolve(gauss_1, gauss_2)
assert np.all(np.abs((gauss_3 - test_gauss_3).array) < 0.01)
def test_convolve_2D_kernels(self):
"""
Check if convolving two kernels with each other works correctly.
"""
gauss_1 = Gaussian2DKernel(3)
gauss_2 = Gaussian2DKernel(4)
test_gauss_3 = Gaussian2DKernel(5)
gauss_3 = convolve(gauss_1, gauss_2)
assert np.all(np.abs((gauss_3 - test_gauss_3).array) < 0.01)
@pytest.mark.parametrize(('number'), NUMS)
def test_multiply_scalar(self, number):
"""
Check if multiplying a kernel with a scalar works correctly.
"""
gauss = Gaussian1DKernel(3)
gauss_new = number * gauss
assert_almost_equal(gauss_new.array, gauss.array * number, decimal=12)
@pytest.mark.parametrize(('number'), NUMS)
def test_multiply_scalar_type(self, number):
"""
Check if multiplying a kernel with a scalar works correctly.
"""
gauss = Gaussian1DKernel(3)
gauss_new = number * gauss
assert type(gauss_new) is Gaussian1DKernel
@pytest.mark.parametrize(('number'), NUMS)
def test_rmultiply_scalar_type(self, number):
"""
Check if multiplying a kernel with a scalar works correctly.
"""
gauss = Gaussian1DKernel(3)
gauss_new = gauss * number
assert type(gauss_new) is Gaussian1DKernel
def test_multiply_kernel1d(self):
"""Test that multiplying two 1D kernels raises an exception."""
gauss = Gaussian1DKernel(3)
with pytest.raises(Exception):
gauss * gauss
def test_multiply_kernel2d(self):
"""Test that multiplying two 2D kernels raises an exception."""
gauss = Gaussian2DKernel(3)
with pytest.raises(Exception):
gauss * gauss
def test_multiply_kernel1d_kernel2d(self):
"""
Test that multiplying a 1D kernel with a 2D kernel raises an
exception.
"""
with pytest.raises(Exception):
Gaussian1DKernel(3) * Gaussian2DKernel(3)
def test_add_kernel_scalar(self):
"""Test that adding a scalar to a kernel raises an exception."""
with pytest.raises(Exception):
Gaussian1DKernel(3) + 1
def test_model_1D_kernel(self):
"""
Check Model1DKernel against Gaussian1Dkernel
"""
stddev = 5.
gauss = Gaussian1D(1. / np.sqrt(2 * np.pi * stddev**2), 0, stddev)
model_gauss_kernel = Model1DKernel(gauss, x_size=21)
gauss_kernel = Gaussian1DKernel(stddev, x_size=21)
assert_almost_equal(model_gauss_kernel.array, gauss_kernel.array,
decimal=12)
def test_model_2D_kernel(self):
"""
Check Model2DKernel against Gaussian2Dkernel
"""
stddev = 5.
gauss = Gaussian2D(1. / (2 * np.pi * stddev**2), 0, 0, stddev, stddev)
model_gauss_kernel = Model2DKernel(gauss, x_size=21)
gauss_kernel = Gaussian2DKernel(stddev, x_size=21)
assert_almost_equal(model_gauss_kernel.array, gauss_kernel.array,
decimal=12)
def test_custom_1D_kernel(self):
"""
Check CustomKernel against Box1DKernel.
"""
#Define one dimensional array:
array = np.ones(5)
custom = CustomKernel(array)
custom.normalize()
box = Box1DKernel(5)
c2 = convolve(delta_pulse_1D, custom, boundary='fill')
c1 = convolve(delta_pulse_1D, box, boundary='fill')
assert_almost_equal(c1, c2, decimal=12)
def test_custom_2D_kernel(self):
"""
Check CustomKernel against Box2DKernel.
"""
#Define one dimensional array:
array = np.ones((5, 5))
custom = CustomKernel(array)
custom.normalize()
box = Box2DKernel(5)
c2 = convolve(delta_pulse_2D, custom, boundary='fill')
c1 = convolve(delta_pulse_2D, box, boundary='fill')
assert_almost_equal(c1, c2, decimal=12)
def test_custom_1D_kernel_list(self):
"""
Check if CustomKernel works with lists.
"""
custom = CustomKernel([1, 1, 1, 1, 1])
assert custom.is_bool is True
def test_custom_2D_kernel_list(self):
"""
Check if CustomKernel works with lists.
"""
custom = CustomKernel([[1, 1, 1],
[1, 1, 1],
[1, 1, 1]])
assert custom.is_bool is True
def test_custom_1D_kernel_zerosum(self):
"""
Check if CustomKernel works when the input array/list
sums to zero.
"""
array = [-2, -1, 0, 1, 2]
custom = CustomKernel(array)
custom.normalize()
assert custom.truncation == 0.
assert custom._kernel_sum == 0.
def test_custom_2D_kernel_zerosum(self):
"""
Check if CustomKernel works when the input array/list
sums to zero.
"""
array = [[0, -1, 0], [-1, 4, -1], [0, -1, 0]]
custom = CustomKernel(array)
custom.normalize()
assert custom.truncation == 0.
assert custom._kernel_sum == 0.
def test_custom_kernel_odd_error(self):
"""
Check if CustomKernel raises if the array size is odd.
"""
with pytest.raises(KernelSizeError):
CustomKernel([1, 1, 1, 1])
def test_add_1D_kernels(self):
"""
Check if adding of two 1D kernels works.
"""
box_1 = Box1DKernel(5)
box_2 = Box1DKernel(3)
box_3 = Box1DKernel(1)
box_sum_1 = box_1 + box_2 + box_3
box_sum_2 = box_2 + box_3 + box_1
box_sum_3 = box_3 + box_1 + box_2
ref = [1/5., 1/5. + 1/3., 1 + 1/3. + 1/5., 1/5. + 1/3., 1/5.]
assert_almost_equal(box_sum_1.array, ref, decimal=12)
assert_almost_equal(box_sum_2.array, ref, decimal=12)
assert_almost_equal(box_sum_3.array, ref, decimal=12)
# Assert that the kernels haven't changed
assert_almost_equal(box_1.array, [0.2, 0.2, 0.2, 0.2, 0.2], decimal=12)
assert_almost_equal(box_2.array, [1/3., 1/3., 1/3.], decimal=12)
assert_almost_equal(box_3.array, [1], decimal=12)
def test_add_2D_kernels(self):
"""
Check if adding of two 1D kernels works.
"""
box_1 = Box2DKernel(3)
box_2 = Box2DKernel(1)
box_sum_1 = box_1 + box_2
box_sum_2 = box_2 + box_1
ref = [[1 / 9., 1 / 9., 1 / 9.],
[1 / 9., 1 + 1 / 9., 1 / 9.],
[1 / 9., 1 / 9., 1 / 9.]]
ref_1 = [[1 / 9., 1 / 9., 1 / 9.],
[1 / 9., 1 / 9., 1 / 9.],
[1 / 9., 1 / 9., 1 / 9.]]
assert_almost_equal(box_2.array, [[1]], decimal=12)
assert_almost_equal(box_1.array, ref_1, decimal=12)
assert_almost_equal(box_sum_1.array, ref, decimal=12)
assert_almost_equal(box_sum_2.array, ref, decimal=12)
def test_Gaussian1DKernel_even_size(self):
"""
Check if even size for GaussianKernel works.
"""
gauss = Gaussian1DKernel(3, x_size=10)
assert gauss.array.size == 10
def test_Gaussian2DKernel_even_size(self):
"""
Check if even size for GaussianKernel works.
"""
gauss = Gaussian2DKernel(3, x_size=10, y_size=10)
assert gauss.array.shape == (10, 10)
def test_normalize_peak(self):
"""
Check if normalize works with peak mode.
"""
custom = CustomKernel([1, 2, 3, 2, 1])
custom.normalize(mode='peak')
assert custom.array.max() == 1
def test_check_kernel_attributes(self):
"""
Check if kernel attributes are correct.
"""
box = Box2DKernel(5)
# Check truncation
assert box.truncation == 0
# Check model
assert isinstance(box.model, Box2D)
# Check center
assert box.center == [2, 2]
# Check normalization
box.normalize()
assert_almost_equal(box._kernel_sum, 1., decimal=12)
# Check separability
assert box.separable
@pytest.mark.parametrize(('kernel_type', 'mode'), list(itertools.product(KERNEL_TYPES, MODES)))
def test_dicretize_modes(self, kernel_type, mode):
"""
Check if the different modes result in kernels that work with convolve.
Use only small kernel width, to make the test pass quickly.
"""
if kernel_type == AiryDisk2DKernel and not HAS_SCIPY:
pytest.skip("Omitting AiryDisk2DKernel, which requires SciPy")
if not kernel_type == Ring2DKernel:
kernel = kernel_type(3)
else:
kernel = kernel_type(3, 3 * 0.2)
if kernel.dimension == 1:
c1 = convolve_fft(delta_pulse_1D, kernel, boundary='fill')
c2 = convolve(delta_pulse_1D, kernel, boundary='fill')
assert_almost_equal(c1, c2, decimal=12)
else:
c1 = convolve_fft(delta_pulse_2D, kernel, boundary='fill')
c2 = convolve(delta_pulse_2D, kernel, boundary='fill')
assert_almost_equal(c1, c2, decimal=12)
@pytest.mark.parametrize(('width'), WIDTHS_EVEN)
def test_box_kernels_even_size(self, width):
"""
Check if BoxKernel work properly with even sizes.
"""
kernel_1D = Box1DKernel(width)
assert kernel_1D.shape[0] % 2 != 0
assert kernel_1D.array.sum() == 1.
kernel_2D = Box2DKernel(width)
assert np.all([_ % 2 != 0 for _ in kernel_2D.shape])
assert kernel_2D.array.sum() == 1.
def test_kernel_normalization(self):
"""
Test that repeated normalizations do not change the kernel [#3747].
"""
kernel = CustomKernel(np.ones(5))
kernel.normalize()
data = np.copy(kernel.array)
kernel.normalize()
assert_allclose(data, kernel.array)
kernel.normalize()
assert_allclose(data, kernel.array)
def test_kernel_normalization_mode(self):
"""
Test that an error is raised if mode is invalid.
"""
with pytest.raises(ValueError):
kernel = CustomKernel(np.ones(3))
kernel.normalize(mode='invalid')
def test_kernel1d_int_size(self):
"""
Test that an error is raised if ``Kernel1D`` ``x_size`` is not
an integer.
"""
with pytest.raises(TypeError):
Gaussian1DKernel(3, x_size=1.2)
def test_kernel2d_int_xsize(self):
"""
Test that an error is raised if ``Kernel2D`` ``x_size`` is not
an integer.
"""
with pytest.raises(TypeError):
Gaussian2DKernel(3, x_size=1.2)
def test_kernel2d_int_ysize(self):
"""
Test that an error is raised if ``Kernel2D`` ``y_size`` is not
an integer.
"""
with pytest.raises(TypeError):
Gaussian2DKernel(3, x_size=5, y_size=1.2)
def test_kernel1d_initialization(self):
"""
Test that an error is raised if an array or model is not
specified for ``Kernel1D``.
"""
with pytest.raises(TypeError):
Kernel1D()
def test_kernel2d_initialization(self):
"""
Test that an error is raised if an array or model is not
specified for ``Kernel2D``.
"""
with pytest.raises(TypeError):
Kernel2D()
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