import itertools

import numpy as np
import pytest
from numpy.testing import assert_array_almost_equal, assert_array_equal, assert_equal
from scipy import ndimage as ndi

from skimage._shared._warnings import expected_warnings
from skimage.feature import peak


np.random.seed(21)


class TestPeakLocalMax:
    def test_trivial_case(self):
        trivial = np.zeros((25, 25))
        peak_indices = peak.peak_local_max(trivial, min_distance=1)
        assert type(peak_indices) is np.ndarray
        assert peak_indices.size == 0

    def test_noisy_peaks(self):
        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(self):
        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_array_almost_equal(peaks, [(3, 3)])

    def test_absolute_threshold(self):
        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_array_almost_equal(peaks, [(3, 3)])

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

    def test_flat_peak(self):
        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_sorted_peaks(self):
        image = np.zeros((5, 5), dtype=np.uint8)
        image[1, 1] = 20
        image[3, 3] = 10
        peaks = peak.peak_local_max(image, min_distance=1)
        assert peaks.tolist() == [[1, 1], [3, 3]]

        image = np.zeros((3, 10))
        image[1, (1, 3, 5, 7)] = (1, 2, 3, 4)
        peaks = peak.peak_local_max(image, min_distance=1)
        assert peaks.tolist() == [[1, 7], [1, 5], [1, 3], [1, 1]]

    def test_num_peaks(self):
        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_peaks_and_labels(self):
        image = np.zeros((7, 7), dtype=np.uint8)
        labels = np.zeros((7, 7), dtype=np.uint8) + 20
        image[1, 1] = 10
        image[1, 3] = 11
        image[1, 5] = 12
        image[3, 5] = 8
        image[5, 3] = 7
        peaks_limited = peak.peak_local_max(
            image, min_distance=1, threshold_abs=0, labels=labels
        )
        assert len(peaks_limited) == 5
        peaks_limited = peak.peak_local_max(
            image, min_distance=1, threshold_abs=0, labels=labels, num_peaks=2
        )
        assert len(peaks_limited) == 2

    def test_num_peaks_tot_vs_labels_4quadrants(self):
        np.random.seed(21)
        image = np.random.uniform(size=(20, 30))
        i, j = np.mgrid[0:20, 0:30]
        labels = 1 + (i >= 10) + (j >= 15) * 2
        result = peak.peak_local_max(
            image,
            labels=labels,
            min_distance=1,
            threshold_rel=0,
            num_peaks=np.inf,
            num_peaks_per_label=2,
        )
        assert len(result) == 8
        result = peak.peak_local_max(
            image,
            labels=labels,
            min_distance=1,
            threshold_rel=0,
            num_peaks=np.inf,
            num_peaks_per_label=1,
        )
        assert len(result) == 4
        result = peak.peak_local_max(
            image,
            labels=labels,
            min_distance=1,
            threshold_rel=0,
            num_peaks=2,
            num_peaks_per_label=2,
        )
        assert len(result) == 2

    def test_num_peaks3D(self):
        # 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(self):
        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
        peak_idx = peak.peak_local_max(
            image,
            labels=labels,
            min_distance=1,
            threshold_rel=0,
            footprint=footprint,
            exclude_border=False,
        )
        result = np.zeros_like(expected, dtype=bool)
        result[tuple(peak_idx.T)] = True
        assert (result == expected).all()

    def test_indices_with_labels(self):
        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 = np.stack(np.nonzero(expected == image), axis=-1)
        expected = expected[np.argsort(image[tuple(expected.T)])[::-1]]
        result = peak.peak_local_max(
            image,
            labels=labels,
            min_distance=1,
            threshold_rel=0,
            footprint=footprint,
            exclude_border=False,
        )
        result = result[np.argsort(image[tuple(result.T)])[::-1]]
        assert (result == expected).all()

    def test_ndarray_exclude_border(self):
        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.array([[2, 2, 2]], dtype=int)
        expectedNoBorder = np.array([[0, 0, 1], [2, 2, 2], [3, 0, 0]], dtype=int)
        result = peak.peak_local_max(nd_image, min_distance=2, exclude_border=2)
        assert_array_equal(result, expected)
        # Check that bools work as expected
        assert_array_equal(
            peak.peak_local_max(nd_image, min_distance=2, exclude_border=2),
            peak.peak_local_max(nd_image, min_distance=2, exclude_border=True),
        )
        assert_array_equal(
            peak.peak_local_max(nd_image, min_distance=2, exclude_border=0),
            peak.peak_local_max(nd_image, min_distance=2, exclude_border=False),
        )

        # Check both versions with no border
        result = peak.peak_local_max(nd_image, min_distance=2, exclude_border=0)
        assert_array_equal(result, expectedNoBorder)
        peak_idx = peak.peak_local_max(nd_image, exclude_border=False)
        result = np.zeros_like(nd_image, dtype=bool)
        result[tuple(peak_idx.T)] = True
        assert_array_equal(result, nd_image.astype(bool))

    def test_empty(self):
        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,
            exclude_border=False,
        )
        assert result.shape == (0, image.ndim)

    def test_empty_non2d_indices(self):
        image = np.zeros((10, 10, 10))
        result = peak.peak_local_max(
            image,
            footprint=np.ones((3, 3, 3), bool),
            min_distance=1,
            threshold_rel=0,
            exclude_border=False,
        )
        assert result.shape == (0, image.ndim)

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

    def test_adjacent_and_same(self):
        image = np.zeros((10, 20))
        labels = np.zeros((10, 20), int)
        image[5, 5:6] = 1
        labels[5, 5:6] = 1
        expected = np.stack(np.where(labels == 1), axis=-1)
        result = peak.peak_local_max(
            image,
            labels=labels,
            footprint=np.ones((3, 3), bool),
            min_distance=1,
            threshold_rel=0,
            exclude_border=False,
        )
        assert_array_equal(result, expected)

    def test_adjacent_and_different(self):
        image = np.zeros((10, 20))
        labels = np.zeros((10, 20), int)
        image[5, 5] = 1
        image[5, 6] = 0.5
        labels[5, 5:6] = 1
        expected = np.stack(np.where(image == 1), axis=-1)
        result = peak.peak_local_max(
            image,
            labels=labels,
            footprint=np.ones((3, 3), bool),
            min_distance=1,
            threshold_rel=0,
            exclude_border=False,
        )
        assert_array_equal(result, expected)
        result = peak.peak_local_max(
            image, labels=labels, min_distance=1, threshold_rel=0, exclude_border=False
        )
        assert_array_equal(result, expected)

    def test_not_adjacent_and_different(self):
        image = np.zeros((10, 20))
        labels = np.zeros((10, 20), int)
        image[5, 5] = 1
        image[5, 8] = 0.5
        labels[image > 0] = 1
        expected = np.stack(np.where(labels == 1), axis=-1)
        result = peak.peak_local_max(
            image,
            labels=labels,
            footprint=np.ones((3, 3), bool),
            min_distance=1,
            threshold_rel=0,
            exclude_border=False,
        )
        assert_array_equal(result, expected)

    def test_two_objects(self):
        image = np.zeros((10, 20))
        labels = np.zeros((10, 20), int)
        image[5, 5] = 1
        image[5, 15] = 0.5
        labels[5, 5] = 1
        labels[5, 15] = 2
        expected = np.stack(np.where(labels > 0), axis=-1)
        result = peak.peak_local_max(
            image,
            labels=labels,
            footprint=np.ones((3, 3), bool),
            min_distance=1,
            threshold_rel=0,
            exclude_border=False,
        )
        assert_array_equal(result, expected)

    def test_adjacent_different_objects(self):
        image = np.zeros((10, 20))
        labels = np.zeros((10, 20), int)
        image[5, 5] = 1
        image[5, 6] = 0.5
        labels[5, 5] = 1
        labels[5, 6] = 2
        expected = np.stack(np.where(labels > 0), axis=-1)
        result = peak.peak_local_max(
            image,
            labels=labels,
            footprint=np.ones((3, 3), bool),
            min_distance=1,
            threshold_rel=0,
            exclude_border=False,
        )
        assert_array_equal(result, expected)

    def test_four_quadrants(self):
        image = np.random.uniform(size=(20, 30))
        i, j = np.mgrid[0:20, 0:30]
        labels = 1 + (i >= 10) + (j >= 15) * 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, 10), (10, 20)):
            for jmin, jmax in ((0, 15), (15, 30)):
                expected[imin:imax, jmin:jmax] = ndi.maximum_filter(
                    image[imin:imax, jmin:jmax], footprint=footprint
                )
        expected = expected == image
        peak_idx = peak.peak_local_max(
            image,
            labels=labels,
            footprint=footprint,
            min_distance=1,
            threshold_rel=0,
            exclude_border=False,
        )
        result = np.zeros_like(image, dtype=bool)
        result[tuple(peak_idx.T)] = True
        assert np.all(result == expected)

    def test_disk(self):
        '''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]])
        peak_idx = peak.peak_local_max(
            image,
            labels=np.ones((10, 20), int),
            footprint=footprint,
            min_distance=1,
            threshold_rel=0,
            threshold_abs=-1,
            exclude_border=False,
        )
        result = np.zeros_like(image, dtype=bool)
        result[tuple(peak_idx.T)] = True
        assert np.all(result)
        peak_idx = peak.peak_local_max(
            image, footprint=footprint, threshold_abs=-1, exclude_border=False
        )
        result = np.zeros_like(image, dtype=bool)
        result[tuple(peak_idx.T)] = True
        assert np.all(result)

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

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

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

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

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

        image[2, 2] = 0
        with expected_warnings(["When min_distance < 1"]):
            assert len(peak.peak_local_max(image, min_distance=0)) == image.size - 1

    def test_peak_at_border(self):
        image = np.full((10, 10), -2)
        image[2, 4] = -1
        image[3, 0] = -1

        peaks = peak.peak_local_max(image, min_distance=3)
        assert peaks.size == 0

        peaks = peak.peak_local_max(image, min_distance=3, exclude_border=0)
        assert len(peaks) == 2
        assert [2, 4] in peaks
        assert [3, 0] in peaks


@pytest.mark.parametrize(
    ["indices"],
    [[indices] for indices in itertools.product(range(5), range(5))],
)
def test_exclude_border(indices):
    image = np.zeros((5, 5))
    image[indices] = 1

    # exclude_border = False, means it will always be found.
    assert len(peak.peak_local_max(image, exclude_border=False)) == 1

    # exclude_border = 0, means it will always be found.
    assert len(peak.peak_local_max(image, exclude_border=0)) == 1

    # exclude_border = True, min_distance=1 means it will be found unless it's
    # on the edge.
    if indices[0] in (0, 4) or indices[1] in (0, 4):
        expected_peaks = 0
    else:
        expected_peaks = 1
    assert (
        len(peak.peak_local_max(image, min_distance=1, exclude_border=True))
        == expected_peaks
    )

    # exclude_border = (1, 0) means it will be found unless it's on the edge of
    # the first dimension.
    if indices[0] in (0, 4):
        expected_peaks = 0
    else:
        expected_peaks = 1
    assert len(peak.peak_local_max(image, exclude_border=(1, 0))) == expected_peaks

    # exclude_border = (0, 1) means it will be found unless it's on the edge of
    # the second dimension.
    if indices[1] in (0, 4):
        expected_peaks = 0
    else:
        expected_peaks = 1
    assert len(peak.peak_local_max(image, exclude_border=(0, 1))) == expected_peaks


def test_exclude_border_errors():
    image = np.zeros((5, 5))

    # exclude_border doesn't have the right cardinality.
    with pytest.raises(ValueError):
        assert peak.peak_local_max(image, exclude_border=(1,))

    # exclude_border doesn't have the right type
    with pytest.raises(TypeError):
        assert peak.peak_local_max(image, exclude_border=1.0)

    # exclude_border is a tuple of the right cardinality but contains
    # non-integer values.
    with pytest.raises(ValueError):
        assert peak.peak_local_max(image, exclude_border=(1, 'a'))

    # exclude_border is a tuple of the right cardinality but contains a
    # negative value.
    with pytest.raises(ValueError):
        assert peak.peak_local_max(image, exclude_border=(1, -1))

    # exclude_border is a negative value.
    with pytest.raises(ValueError):
        assert peak.peak_local_max(image, exclude_border=-1)


def test_input_values_with_labels():
    # Issue #5235: input values may be modified when labels are used

    img = np.random.rand(128, 128)
    labels = np.zeros((128, 128), int)

    labels[10:20, 10:20] = 1
    labels[12:16, 12:16] = 0

    img_before = img.copy()

    _ = peak.peak_local_max(img, labels=labels)

    assert_array_equal(img, img_before)


class TestProminentPeaks:
    def test_isolated_peaks(self):
        image = np.zeros((15, 15))
        x0, y0, i0 = (12, 8, 1)
        x1, y1, i1 = (2, 2, 1)
        x2, y2, i2 = (5, 13, 1)
        image[y0, x0] = i0
        image[y1, x1] = i1
        image[y2, x2] = i2
        out = peak._prominent_peaks(image)
        assert len(out[0]) == 3
        for i, x, y in zip(out[0], out[1], out[2]):
            assert i in (i0, i1, i2)
            assert x in (x0, x1, x2)
            assert y in (y0, y1, y2)

    def test_threshold(self):
        image = np.zeros((15, 15))
        x0, y0, i0 = (12, 8, 10)
        x1, y1, i1 = (2, 2, 8)
        x2, y2, i2 = (5, 13, 10)
        image[y0, x0] = i0
        image[y1, x1] = i1
        image[y2, x2] = i2
        out = peak._prominent_peaks(image, threshold=None)
        assert len(out[0]) == 3
        for i, x, y in zip(out[0], out[1], out[2]):
            assert i in (i0, i1, i2)
            assert x in (x0, x1, x2)
        out = peak._prominent_peaks(image, threshold=9)
        assert len(out[0]) == 2
        for i, x, y in zip(out[0], out[1], out[2]):
            assert i in (i0, i2)
            assert x in (x0, x2)
            assert y in (y0, y2)

    def test_peaks_in_contact(self):
        image = np.zeros((15, 15))
        x0, y0, i0 = (8, 8, 1)
        x1, y1, i1 = (7, 7, 1)  # prominent peak
        x2, y2, i2 = (6, 6, 1)
        image[y0, x0] = i0
        image[y1, x1] = i1
        image[y2, x2] = i2
        out = peak._prominent_peaks(
            image,
            min_xdistance=3,
            min_ydistance=3,
        )
        assert_equal(out[0], np.array((i1,)))
        assert_equal(out[1], np.array((x1,)))
        assert_equal(out[2], np.array((y1,)))

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

    def test_many_objects(self):
        mask = np.zeros([500, 500], dtype=bool)
        x, y = np.indices((500, 500))
        x_c = x // 20 * 20 + 10
        y_c = y // 20 * 20 + 10
        mask[(x - x_c) ** 2 + (y - y_c) ** 2 < 8**2] = True
        labels, num_objs = ndi.label(mask)
        dist = ndi.distance_transform_edt(mask)
        local_max = peak.peak_local_max(
            dist, min_distance=20, exclude_border=False, labels=labels
        )
        assert len(local_max) == 625