import numpy as np
from numpy.testing import (assert_array_almost_equal as assert_close,
                           assert_equal, assert_raises)
from scipy import ndimage as ndi
from skimage.feature import peak


np.random.seed(21)


def test_trivial_case():
    trivial = np.zeros((25, 25))
    peak_indices = peak.peak_local_max(trivial, min_distance=1, indices=True)
    assert type(peak_indices) is np.ndarray
    assert not peak_indices     # inherent boolean-ness of empty list
    peaks = peak.peak_local_max(trivial, min_distance=1, indices=False)
    assert (peaks.astype(np.bool) == trivial).all()


def test_noisy_peaks():
    peak_locations = [(7, 7), (7, 13), (13, 7), (13, 13)]

    # image with noise of amplitude 0.8 and peaks of amplitude 1
    image = 0.8 * np.random.rand(20, 20)
    for r, c in peak_locations:
        image[r, c] = 1

    peaks_detected = peak.peak_local_max(image, min_distance=5)

    assert len(peaks_detected) == len(peak_locations)
    for loc in peaks_detected:
        assert tuple(loc) in peak_locations


def test_relative_threshold():
    image = np.zeros((5, 5), dtype=np.uint8)
    image[1, 1] = 10
    image[3, 3] = 20
    peaks = peak.peak_local_max(image, min_distance=1, threshold_rel=0.5)
    assert len(peaks) == 1
    assert_close(peaks, [(3, 3)])


def test_absolute_threshold():
    image = np.zeros((5, 5), dtype=np.uint8)
    image[1, 1] = 10
    image[3, 3] = 20
    peaks = peak.peak_local_max(image, min_distance=1, threshold_abs=10)
    assert len(peaks) == 1
    assert_close(peaks, [(3, 3)])


def test_constant_image():
    image = 128 * np.ones((20, 20), dtype=np.uint8)
    peaks = peak.peak_local_max(image, min_distance=1)
    assert len(peaks) == 0


def test_flat_peak():
    image = np.zeros((5, 5), dtype=np.uint8)
    image[1:3, 1:3] = 10
    peaks = peak.peak_local_max(image, min_distance=1)
    assert len(peaks) == 4


def test_num_peaks():
    image = np.zeros((7, 7), dtype=np.uint8)
    image[1, 1] = 10
    image[1, 3] = 11
    image[1, 5] = 12
    image[3, 5] = 8
    image[5, 3] = 7
    assert len(peak.peak_local_max(image, min_distance=1, threshold_abs=0)) == 5
    peaks_limited = peak.peak_local_max(
        image, min_distance=1, threshold_abs=0, num_peaks=2)
    assert len(peaks_limited) == 2
    assert (1, 3) in peaks_limited
    assert (1, 5) in peaks_limited
    peaks_limited = peak.peak_local_max(
        image, min_distance=1, threshold_abs=0, num_peaks=4)
    assert len(peaks_limited) == 4
    assert (1, 3) in peaks_limited
    assert (1, 5) in peaks_limited
    assert (1, 1) in peaks_limited
    assert (3, 5) in peaks_limited


def test_num_peaks3D():
    # Issue 1354: the old code only hold for 2D arrays
    # and this code would die with IndexError
    image = np.zeros((10, 10, 100))
    image[5,5,::5] = np.arange(20)
    peaks_limited = peak.peak_local_max(image, min_distance=1, num_peaks=2)
    assert len(peaks_limited) == 2


def test_reorder_labels():
    image = np.random.uniform(size=(40, 60))
    i, j = np.mgrid[0:40, 0:60]
    labels = 1 + (i >= 20) + (j >= 30) * 2
    labels[labels == 4] = 5
    i, j = np.mgrid[-3:4, -3:4]
    footprint = (i * i + j * j <= 9)
    expected = np.zeros(image.shape, float)
    for imin, imax in ((0, 20), (20, 40)):
        for jmin, jmax in ((0, 30), (30, 60)):
            expected[imin:imax, jmin:jmax] = ndi.maximum_filter(
                            image[imin:imax, jmin:jmax], footprint=footprint)
    expected = (expected == image)
    result = peak.peak_local_max(image, labels=labels, min_distance=1,
                                 threshold_rel=0, footprint=footprint,
                                 indices=False, exclude_border=False)
    assert (result == expected).all()


def test_indices_with_labels():
    image = np.random.uniform(size=(40, 60))
    i, j = np.mgrid[0:40, 0:60]
    labels = 1 + (i >= 20) + (j >= 30) * 2
    i, j = np.mgrid[-3:4, -3:4]
    footprint = (i * i + j * j <= 9)
    expected = np.zeros(image.shape, float)
    for imin, imax in ((0, 20), (20, 40)):
        for jmin, jmax in ((0, 30), (30, 60)):
            expected[imin:imax, jmin:jmax] = ndi.maximum_filter(
                image[imin:imax, jmin:jmax], footprint=footprint)
    expected = (expected == image)
    result = peak.peak_local_max(image, labels=labels, min_distance=1,
                                 threshold_rel=0, footprint=footprint,
                                 indices=True, exclude_border=False)
    assert (result == np.transpose(expected.nonzero())).all()


def test_ndarray_indices_false():
    nd_image = np.zeros((5,5,5))
    nd_image[2,2,2] = 1
    peaks = peak.peak_local_max(nd_image, min_distance=1, indices=False)
    assert (peaks == nd_image.astype(np.bool)).all()


def test_ndarray_exclude_border():
    nd_image = np.zeros((5,5,5))
    nd_image[[1,0,0],[0,1,0],[0,0,1]] = 1
    nd_image[3,0,0] = 1
    nd_image[2,2,2] = 1
    expected = np.zeros_like(nd_image, dtype=np.bool)
    expected[2,2,2] = True
    expectedNoBorder = nd_image > 0
    result = peak.peak_local_max(nd_image, min_distance=2,
        exclude_border=2, indices=False)
    assert_equal(result, expected)
    # Check that bools work as expected
    assert_equal(
        peak.peak_local_max(nd_image, min_distance=2,
            exclude_border=2, indices=False),
        peak.peak_local_max(nd_image, min_distance=2,
            exclude_border=True, indices=False)
        )
    assert_equal(
        peak.peak_local_max(nd_image, min_distance=2,
            exclude_border=0, indices=False),
        peak.peak_local_max(nd_image, min_distance=2,
            exclude_border=False, indices=False)
        )
    # Check both versions with  no border
    assert_equal(
        peak.peak_local_max(nd_image, min_distance=2,
            exclude_border=0, indices=False),
        expectedNoBorder,
        )
    assert_equal(
        peak.peak_local_max(nd_image,
            exclude_border=False, indices=False),
        expectedNoBorder,
        )


def test_empty():
    image = np.zeros((10, 20))
    labels = np.zeros((10, 20), int)
    result = peak.peak_local_max(image, labels=labels,
                                 footprint=np.ones((3, 3), bool),
                                 min_distance=1, threshold_rel=0,
                                 indices=False, exclude_border=False)
    assert np.all(~ result)


def test_one_point():
    image = np.zeros((10, 20))
    labels = np.zeros((10, 20), int)
    image[5, 5] = 1
    labels[5, 5] = 1
    result = peak.peak_local_max(image, labels=labels,
                                 footprint=np.ones((3, 3), bool),
                                 min_distance=1, threshold_rel=0,
                                 indices=False, exclude_border=False)
    assert np.all(result == (labels == 1))


def test_adjacent_and_same():
    image = np.zeros((10, 20))
    labels = np.zeros((10, 20), int)
    image[5, 5:6] = 1
    labels[5, 5:6] = 1
    result = peak.peak_local_max(image, labels=labels,
                                 footprint=np.ones((3, 3), bool),
                                 min_distance=1, threshold_rel=0,
                                 indices=False, exclude_border=False)
    assert np.all(result == (labels == 1))


def test_adjacent_and_different():
    image = np.zeros((10, 20))
    labels = np.zeros((10, 20), int)
    image[5, 5] = 1
    image[5, 6] = .5
    labels[5, 5:6] = 1
    expected = (image == 1)
    result = peak.peak_local_max(image, labels=labels,
                                 footprint=np.ones((3, 3), bool),
                                 min_distance=1, threshold_rel=0,
                                 indices=False, exclude_border=False)
    assert np.all(result == expected)
    result = peak.peak_local_max(image, labels=labels,
                                 min_distance=1, threshold_rel=0,
                                 indices=False, exclude_border=False)
    assert np.all(result == expected)


def test_not_adjacent_and_different():
    image = np.zeros((10, 20))
    labels = np.zeros((10, 20), int)
    image[5, 5] = 1
    image[5, 8] = .5
    labels[image > 0] = 1
    expected = (labels == 1)
    result = peak.peak_local_max(image, labels=labels,
                                 footprint=np.ones((3, 3), bool),
                                 min_distance=1, threshold_rel=0,
                                 indices=False, exclude_border=False)
    assert np.all(result == expected)


def test_two_objects():
    image = np.zeros((10, 20))
    labels = np.zeros((10, 20), int)
    image[5, 5] = 1
    image[5, 15] = .5
    labels[5, 5] = 1
    labels[5, 15] = 2
    expected = (labels > 0)
    result = peak.peak_local_max(image, labels=labels,
                                 footprint=np.ones((3, 3), bool),
                                 min_distance=1, threshold_rel=0,
                                 indices=False, exclude_border=False)
    assert np.all(result == expected)


def test_adjacent_different_objects():
    image = np.zeros((10, 20))
    labels = np.zeros((10, 20), int)
    image[5, 5] = 1
    image[5, 6] = .5
    labels[5, 5] = 1
    labels[5, 6] = 2
    expected = (labels > 0)
    result = peak.peak_local_max(image, labels=labels,
                                 footprint=np.ones((3, 3), bool),
                                 min_distance=1, threshold_rel=0,
                                 indices=False, exclude_border=False)
    assert np.all(result == expected)


def test_four_quadrants():
    image = np.random.uniform(size=(40, 60))
    i, j = np.mgrid[0:40, 0:60]
    labels = 1 + (i >= 20) + (j >= 30) * 2
    i, j = np.mgrid[-3:4, -3:4]
    footprint = (i * i + j * j <= 9)
    expected = np.zeros(image.shape, float)
    for imin, imax in ((0, 20), (20, 40)):
        for jmin, jmax in ((0, 30), (30, 60)):
            expected[imin:imax, jmin:jmax] = ndi.maximum_filter(
                image[imin:imax, jmin:jmax], footprint=footprint)
    expected = (expected == image)
    result = peak.peak_local_max(image, labels=labels, footprint=footprint,
                                 min_distance=1, threshold_rel=0,
                                 indices=False, exclude_border=False)
    assert np.all(result == expected)


def test_disk():
    '''regression test of img-1194, footprint = [1]
    Test peak.peak_local_max when every point is a local maximum
    '''
    image = np.random.uniform(size=(10, 20))
    footprint = np.array([[1]])
    result = peak.peak_local_max(image, labels=np.ones((10, 20)),
                                 footprint=footprint,
                                 min_distance=1, threshold_rel=0,
                                 threshold_abs=-1, indices=False,
                                 exclude_border=False)
    assert np.all(result)
    result = peak.peak_local_max(image, footprint=footprint, threshold_abs=-1,
                                 indices=False, exclude_border=False)
    assert np.all(result)


def test_3D():
    image = np.zeros((30, 30, 30))
    image[15, 15, 15] = 1
    image[5, 5, 5] = 1
    assert_equal(peak.peak_local_max(image, min_distance=10, threshold_rel=0),
                 [[15, 15, 15]])
    assert_equal(peak.peak_local_max(image, min_distance=6, threshold_rel=0),
                 [[15, 15, 15]])
    assert_equal(peak.peak_local_max(image, min_distance=10, threshold_rel=0,
                                     exclude_border=False),
                 [[5, 5, 5], [15, 15, 15]])
    assert_equal(peak.peak_local_max(image, min_distance=5, threshold_rel=0),
                 [[5, 5, 5], [15, 15, 15]])


def test_4D():
    image = np.zeros((30, 30, 30, 30))
    image[15, 15, 15, 15] = 1
    image[5, 5, 5, 5] = 1
    assert_equal(peak.peak_local_max(image, min_distance=10, threshold_rel=0),
                 [[15, 15, 15, 15]])
    assert_equal(peak.peak_local_max(image, min_distance=6, threshold_rel=0),
                 [[15, 15, 15, 15]])
    assert_equal(peak.peak_local_max(image, min_distance=10, threshold_rel=0,
                                     exclude_border=False),
                 [[5, 5, 5, 5], [15, 15, 15, 15]])
    assert_equal(peak.peak_local_max(image, min_distance=5, threshold_rel=0),
                 [[5, 5, 5, 5], [15, 15, 15, 15]])


def test_threshold_rel_default():
    image = np.ones((5, 5))

    image[2, 2] = 1
    assert len(peak.peak_local_max(image)) == 0

    image[2, 2] = 2
    assert_equal(peak.peak_local_max(image), [[2, 2]])

    image[2, 2] = 0
    assert len(peak.peak_local_max(image, min_distance=0)) == image.size - 1


if __name__ == '__main__':
    from numpy import testing
    testing.run_module_suite()
