def test_masked_registration_random_masks_non_equal_sizes():
    """masked_register_translation should be able to register
    translations between images that are not the same size even
    with random masks."""
    # See random number generator for reproducible results
    np.random.seed(23)

    reference_image = camera()
    shift = (-7, 12)
    shifted = np.real(np.fft.ifft2(fourier_shift(
        np.fft.fft2(reference_image), shift)))

    # Crop the shifted image
    shifted = shifted[64:-64, 64:-64]

    # Random masks with 75% of pixels being valid
    ref_mask = np.random.choice(
        [True, False], reference_image.shape, p=[3 / 4, 1 / 4])
    shifted_mask = np.random.choice(
        [True, False], shifted.shape, p=[3 / 4, 1 / 4])

    measured_shift = masked_register_translation(
        reference_image,
        shifted,
        np.ones_like(ref_mask),
        np.ones_like(shifted_mask))
    assert_equal(measured_shift, -np.array(shift))

def test_masked_registration_padfield_data():
    """ Masked translation registration should behave like in the original 
    publication """
    # Test translated from MATLABimplementation `MaskedFFTRegistrationTest` 
    # file. You can find the source code here: 
    # http://www.dirkpadfield.com/Home/MaskedFFTRegistrationCode.zip

    shifts = [(75, 75), (-130, 130), (130, 130)]
    for xi, yi in shifts:
        
        fixed_image = imread(
            IMAGES_DIR / 'OriginalX{:d}Y{:d}.png'.format(xi, yi))
        moving_image = imread(
            IMAGES_DIR / 'TransformedX{:d}Y{:d}.png'.format(xi, yi))

        # Valid pixels are 1
        fixed_mask = (fixed_image != 0)
        moving_mask = (moving_image != 0)

        # Note that shifts in x and y and shifts in cols and rows
        shift_y, shift_x = masked_register_translation(fixed_image, 
                                                       moving_image, 
                                                       fixed_mask, 
                                                       moving_mask, 
                                                       overlap_ratio = 1/10)
        # Note: by looking at the test code from Padfield's 
        # MaskedFFTRegistrationCode repository, the 
        # shifts were not xi and yi, but xi and -yi
        assert_equal((shift_x, shift_y), (-xi, yi))

def test_binary_descriptors_rotation_crosscheck_true():
    """Verify matched keypoints and their corresponding masks results between
    image and its rotated version with the expected keypoint pairs with
    cross_check enabled."""
    img = data.astronaut()
    img = rgb2gray(img)
    tform = tf.SimilarityTransform(scale=1, rotation=0.15, translation=(0, 0))
    rotated_img = tf.warp(img, tform, clip=False)

    extractor = BRIEF(descriptor_size=512)

    keypoints1 = corner_peaks(corner_harris(img), min_distance=5,
                              threshold_abs=0, threshold_rel=0.1)
    extractor.extract(img, keypoints1)
    descriptors1 = extractor.descriptors

    keypoints2 = corner_peaks(corner_harris(rotated_img), min_distance=5,
                              threshold_abs=0, threshold_rel=0.1)
    extractor.extract(rotated_img, keypoints2)
    descriptors2 = extractor.descriptors

    matches = match_descriptors(descriptors1, descriptors2, cross_check=True)

    exp_matches1 = np.array([ 0,  2,  3,  4,  5,  6,  9, 11, 12, 13, 14, 17,
                             18, 19, 21, 22, 23, 26, 27, 28, 29, 31, 32, 33,
                             34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46])
    exp_matches2 = np.array([ 0,  2,  3,  1,  4,  6,  5,  7, 13, 10,  9, 11,
                             15,  8, 14, 12, 16, 18, 19, 21, 20, 24, 25, 26,
                             28, 27, 22, 23, 29, 30, 31, 32, 35, 33, 34, 36])
    assert_equal(matches[:, 0], exp_matches1)
    assert_equal(matches[:, 1], exp_matches2)

def test_subdivide_polygon():
    new_square1 = square
    new_square2 = square[:-1]
    new_square3 = square[:-1]
    # test iterative subdvision
    for _ in range(10):
        square1, square2, square3 = new_square1, new_square2, new_square3
        # test different B-Spline degrees
        for degree in range(1, 7):
            mask_len = len(_SUBDIVISION_MASKS[degree][0])
            # test circular
            new_square1 = subdivide_polygon(square1, degree)
            assert_array_equal(new_square1[-1], new_square1[0])
            assert_equal(new_square1.shape[0],
                         2 * square1.shape[0] - 1)
            # test non-circular
            new_square2 = subdivide_polygon(square2, degree)
            assert_equal(new_square2.shape[0],
                         2 * (square2.shape[0] - mask_len + 1))
            # test non-circular, preserve_ends
            new_square3 = subdivide_polygon(square3, degree, True)
            assert_equal(new_square3[0], square3[0])
            assert_equal(new_square3[-1], square3[-1])

            assert_equal(new_square3.shape[0],
                         2 * (square3.shape[0] - mask_len + 2))

    # not supported B-Spline degree
    with testing.raises(ValueError):
        subdivide_polygon(square, 0)
    with testing.raises(ValueError):
        subdivide_polygon(square, 8)

 def test_hdx_rgb_roundtrip(self):
     from skimage.color.colorconv import hdx_from_rgb, rgb_from_hdx
     img_rgb = self.img_rgb
     conv = combine_stains(separate_stains(img_rgb, hdx_from_rgb),
                           rgb_from_hdx)
     with expected_warnings(['precision loss']):
         assert_equal(img_as_ubyte(conv), img_rgb)

def test_binary_descriptors():
    descs1 = np.array([[True, True, False, True, True],
                       [False, True, False, True, True]])
    descs2 = np.array([[True, False, False, True, False],
                       [False, False, True, True, True]])
    matches = match_descriptors(descs1, descs2)
    assert_equal(matches, [[0, 0], [1, 1]])

def test_basic():
    x = np.array([[1, 1, 3],
                  [0, 2, 0],
                  [4, 3, 1]])
    path, cost = spath.shortest_path(x)
    assert_array_equal(path, [0, 0, 1])
    assert_equal(cost, 1)

def test_reach():
    x = np.array([[1, 1, 3],
                  [0, 2, 0],
                  [4, 3, 1]])
    path, cost = spath.shortest_path(x, reach=2)
    assert_array_equal(path, [0, 0, 2])
    assert_equal(cost, 0)

def test_imexport_imimport():
    shape = (2, 2)
    image = np.zeros(shape)
    with expected_warnings(['precision loss']):
        pil_image = ndarray_to_pil(image)
    out = pil_to_ndarray(pil_image)
    assert_equal(out.shape, shape)

 def test_rectangle_selem(self):
     """Test rectangle structuring elements"""
     for i in range(0, 5):
         for j in range(0, 5):
             actual_mask = selem.rectangle(i, j)
             expected_mask = np.ones((i, j), dtype='uint8')
             assert_equal(expected_mask, actual_mask)

def test_string_sort():
    filenames = ['f9.10.png', 'f9.9.png', 'f10.10.png', 'f10.9.png',
                 'e9.png', 'e10.png', 'em.png']
    sorted_filenames = ['e9.png', 'e10.png', 'em.png', 'f9.9.png',
                        'f9.10.png', 'f10.9.png', 'f10.10.png']
    sorted_filenames = sorted(filenames, key=alphanumeric_key)
    assert_equal(sorted_filenames, sorted_filenames)

def test_pad_input():
    """Test `match_template` when `pad_input=True`.

    This test places two full templates (one with values lower than the image
    mean, the other higher) and two half templates, which are on the edges of
    the image. The two full templates should score the top (positive and
    negative) matches and the centers of the half templates should score 2nd.
    """
    # Float prefactors ensure that image range is between 0 and 1
    template = 0.5 * diamond(2)
    image = 0.5 * np.ones((9, 19))
    mid = slice(2, 7)
    image[mid, :3] -= template[:, -3:]  # half min template centered at 0
    image[mid, 4:9] += template         # full max template centered at 6
    image[mid, -9:-4] -= template       # full min template centered at 12
    image[mid, -3:] += template[:, :3]  # half max template centered at 18

    result = match_template(image, template, pad_input=True,
                            constant_values=image.mean())

    # get the max and min results.
    sorted_result = np.argsort(result.flat)
    i, j = np.unravel_index(sorted_result[:2], result.shape)
    assert_equal(j, (12, 0))
    i, j = np.unravel_index(sorted_result[-2:], result.shape)
    assert_equal(j, (18, 6))

def test_hough_line_angles():
    img = np.zeros((10, 10))
    img[0, 0] = 1

    out, angles, d = transform.hough_line(img, np.linspace(0, 360, 10))

    assert_equal(len(angles), 10)

def test_peak_float_out_of_range_dtype():
    im = np.array([10, 100], dtype=np.float16)
    nbins = 10
    frequencies, bin_centers = exposure.histogram(im, nbins=nbins, source_range='dtype')
    assert_almost_equal(np.min(bin_centers), -0.9, 3)
    assert_almost_equal(np.max(bin_centers), 0.9, 3)
    assert_equal(len(bin_centers), 10)

 def test_median_default_value(self):
     a = np.zeros((3, 3), dtype=np.uint8)
     a[1] = 1
     full_selem = np.ones((3, 3), dtype=np.uint8)
     assert_equal(rank.median(a), rank.median(a, full_selem))
     assert rank.median(a)[1, 1] == 0
     assert rank.median(a, disk(1))[1, 1] == 1

def test_hough_line_peaks_zero_input():
    # Test to make sure empty input doesn't cause a failure
    img = np.zeros((100, 100), dtype='uint8')
    theta = np.linspace(0, np.pi, 100)
    hspace, angles, dists = transform.hough_line(img, theta)
    h, a, d = transform.hough_line_peaks(hspace, angles, dists)
    assert_equal(a, np.array([]))

def test_rect_tool():
    img = data.camera()
    viewer = ImageViewer(img)

    tool = RectangleTool(viewer, maxdist=10)
    tool.extents = (100, 150, 100, 150)

    assert_equal(tool.corners,
                 ((100, 150, 150, 100), (100, 100, 150, 150)))
    assert_equal(tool.extents, (100, 150, 100, 150))
    assert_equal(tool.edge_centers,
                 ((100, 125.0, 150, 125.0), (125.0, 100, 125.0, 150)))
    assert_equal(tool.geometry, (100, 150, 100, 150))

    # grab a corner and move it
    do_event(viewer, 'mouse_press', xdata=100, ydata=100)
    do_event(viewer, 'move', xdata=120, ydata=120)
    do_event(viewer, 'mouse_release')
    # assert_equal(tool.geometry, [120, 150, 120, 150])

    # create a new line
    do_event(viewer, 'mouse_press', xdata=10, ydata=10)
    do_event(viewer, 'move', xdata=100, ydata=100)
    do_event(viewer, 'mouse_release')
    assert_equal(tool.geometry, [10, 100,  10, 100])

def test_regular_grid_3d_8():
    ar = np.zeros((3, 20, 40))
    g = regular_grid(ar.shape, 8)
    assert_equal(g, [slice(1.0, None, 3.0), slice(5.0, None, 10.0),
                     slice(5.0, None, 10.0)])
    ar[g] = 1
    assert_equal(ar.sum(), 8)

def test_denoise_bilateral_nan():
    img = np.full((50, 50), np.NaN)
    # This is in fact an optional warning for our test suite.
    # Python 3.5 will not trigger a warning.
    with expected_warnings([r'invalid|\A\Z']):
        out = restoration.denoise_bilateral(img, multichannel=False)
    assert_equal(img, out)

def test_ssim_patch_range():
    N = 51
    X = (np.random.rand(N, N) * 255).astype(np.uint8)
    Y = (np.random.rand(N, N) * 255).astype(np.uint8)

    assert(ssim(X, Y, win_size=N) < 0.1)
    assert_equal(ssim(X, X, win_size=N), 1)