from typing import Optional
from typing import Union

import numpy as np
from scipy.sparse.coo import coo_matrix

from ._typing_utils import Float
from ._typing_utils import Matrix
from ._utils import coo_matrix_builder


def build_frame_cost_matrix(
    dist_matrix: coo_matrix_builder,
    *,
    track_start_cost: Optional[Float],
    track_end_cost: Optional[Float],
) -> coo_matrix:
    """Build sparce array for frame-linking cost matrix.

    Parameters
    ----------
    dist_matrix : Matrix or `_utils.coo_matrix_builder`
        The distance matrix for points at time t and t+1.
    track_start_cost : Float, optional
        The cost for starting the track (b in Jaqaman et al 2008 NMeth)
    track_end_cost : Float, optional
        The cost for ending the track (d in Jaqaman et al 2008 NMeth)

    Returns
    -------
    cost_matrix : FloatArray
        the cost matrix for frame linking
    """
    M = dist_matrix.shape[0]
    N = dist_matrix.shape[1]

    C = coo_matrix_builder((M + N, N + M), dtype=np.float32)
    C.append_matrix(dist_matrix)

    if track_start_cost is None:
        if len(C.data) > 0:
            track_start_cost = np.max(C.data) * 1.05
        else:
            track_start_cost = 1.05
    if track_end_cost is None:
        if len(C.data) > 0:
            track_end_cost = np.max(C.data) * 1.05
        else:
            track_end_cost = 1.05

    C[np.arange(M, M + N), np.arange(N)] = np.ones(N) * track_end_cost
    C[np.arange(M), np.arange(N, N + M)] = np.ones(M) * track_start_cost
    min_val = np.min(C.data) if len(C.data) > 0 else 0
    C[dist_matrix.col + M, dist_matrix.row + N] = min_val

    return C.to_coo_matrix()


def build_segment_cost_matrix(
    gap_closing_dist_matrix: Union[coo_matrix_builder, Matrix],
    splitting_dist_matrix: Union[coo_matrix_builder, Matrix],
    merging_dist_matrix: Union[coo_matrix_builder, Matrix],
    track_start_cost: Optional[Float],
    track_end_cost: Optional[Float],
    no_splitting_cost: Optional[Float],
    no_merging_cost: Optional[Float],
    alternative_cost_factor: Float = 1.05,
    alternative_cost_percentile: Float = 90,
    alternative_cost_percentile_interpolation: str = "lower",
) -> coo_matrix:
    """Build sparce array for segment-linking cost matrix.

    Parameters
    ----------
    gap_closing_dist_matrix : coo_matrix_builder or Matrix
        The distance matrix for closing gaps between segment i and j.
    splitting_dist_matrix : coo_matrix_builder or Matrix
        The distance matrix for splitting between segment i and time/index j
    merging_dist_matrix : coo_matrix_builder or Matrix
        The distance matrix for merging between segment i and time/index j
    track_start_cost : Float, optional
        The cost for starting the track (b in Jaqaman et al 2008 NMeth)
    track_end_cost : Float, optional
        The cost for ending the track (d in Jaqaman et al 2008 NMeth)
    no_splitting_cost : Float, optional
        The cost to reject splitting (d' in Jaqaman et al 2008 NMeth)
    no_merging_cost : Float, optional
        The cost to reject merging (b' in Jaqaman et al 2008 NMeth)
    alternative_cost_factor: Float
        The factor to calculate the alternative costs, by default 1.05.
    alternative_cost_percentile: Float
        The percentile to calculate the alternative costs, by default 90.
    alternative_cost_percentile_interpolation: str
        The percentile interpolation to calculate the alternative costs,
        by default "lower".
        See `numpy.percentile` for allowed values.

    Returns
    -------
    cost_matrix : Optional[coo_matrix]
        the cost matrix for frame linking, None if not appropriate
    """
    M = gap_closing_dist_matrix.shape[0]
    assert gap_closing_dist_matrix.shape[1] == M
    assert splitting_dist_matrix.shape[0] == M
    assert merging_dist_matrix.shape[0] == M
    N1 = splitting_dist_matrix.shape[1]
    N2 = merging_dist_matrix.shape[1]

    S = 2 * M + N1 + N2

    C = coo_matrix_builder((S, S), dtype=np.float32)

    C.append_matrix(gap_closing_dist_matrix)
    C.append_matrix(splitting_dist_matrix.T, shift=(M, 0))
    C.append_matrix(merging_dist_matrix, shift=(0, M))

    upper_left_size = C.size()
    if upper_left_size == 0:
        return None

    # Note:
    # Though the way of assigning track_start_cost, track_end_cost, no_splitting_cost, no_merging_cost # noqa :
    # and min_val is similar to that of TrackMate (link1, link2), GPL3 of TrackMate does not apply. (See link3 for license discussion.) # noqa :
    #   link1 https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/costmatrix/DefaultCostMatrixCreator.java#L186 # noqa :
    #         https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/costmatrix/JaqamanSegmentCostMatrixCreator.java # noqa:
    #         https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/SparseLAPSegmentTracker.java#L148 # noqa:
    #   link2 (default parameters for alternative_cost_percentile, alternative_cost_factor) # noqa :
    #         https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/TrackerKeys.java # noqa :
    #   link3 https://forum.image.sc/t/linear-assignment-problem-based-tracking-package-in-python/57793 # noqa :
    #         https://web.archive.org/web/20210921134401/https://forum.image.sc/t/linear-assignment-problem-based-tracking-package-in-python/57793 # noqa :

    if (
        track_start_cost is None
        or track_end_cost is None
        or no_splitting_cost is None
        or no_merging_cost is None
    ):
        alternative_cost = (
            np.percentile(
                C.data,
                alternative_cost_percentile,
                interpolation=alternative_cost_percentile_interpolation,
            )
            * alternative_cost_factor
        )
        if track_start_cost is None:
            track_start_cost = alternative_cost
        if track_end_cost is None:
            track_end_cost = alternative_cost
        if no_splitting_cost is None:
            no_splitting_cost = alternative_cost
        if no_merging_cost is None:
            no_merging_cost = alternative_cost

    C[np.arange(M + N1, 2 * M + N1), np.arange(M)] = np.ones(M) * track_start_cost
    C[np.arange(2 * M + N1, S), np.arange(M, M + N2)] = np.ones(N2) * no_merging_cost
    C[np.arange(M), np.arange(M + N2, 2 * M + N2)] = np.ones(M) * track_end_cost
    C[np.arange(M, M + N1), np.arange(2 * M + N2, S)] = np.ones(N1) * no_splitting_cost
    min_val = np.min(
        [track_start_cost, track_end_cost, no_splitting_cost, no_merging_cost]
    )

    upper_left_rows = C.row[:upper_left_size]
    upper_left_cols = C.col[:upper_left_size]
    C[upper_left_cols + M + N1, upper_left_rows + M + N2] = min_val

    return C.to_coo_matrix()

from typing import Optional
from typing import Union

import numpy as np
from scipy.sparse.coo import coo_matrix

from ._typing_utils import Float
from ._typing_utils import Matrix
from ._utils import coo_matrix_builder


def build_frame_cost_matrix(
    dist_matrix: coo_matrix_builder,
    *,
    track_start_cost: Optional[Float],
    track_end_cost: Optional[Float],
) -> coo_matrix:
    """Build sparce array for frame-linking cost matrix.

    Parameters
    ----------
    dist_matrix : Matrix or `_utils.coo_matrix_builder`
        The distance matrix for points at time t and t+1.
    track_start_cost : Float, optional
        The cost for starting the track (b in Jaqaman et al 2008 NMeth)
    track_end_cost : Float, optional
        The cost for ending the track (d in Jaqaman et al 2008 NMeth)

    Returns
    -------
    cost_matrix : FloatArray
        the cost matrix for frame linking
    """
    M = dist_matrix.shape[0]
    N = dist_matrix.shape[1]

    C = coo_matrix_builder((M + N, N + M), dtype=np.float32)
    C.append_matrix(dist_matrix)

    if track_start_cost is None:
        if len(C.data) > 0:
            track_start_cost = np.max(C.data) * 1.05
        else:
            track_start_cost = 1.05
    if track_end_cost is None:
        if len(C.data) > 0:
            track_end_cost = np.max(C.data) * 1.05
        else:
            track_end_cost = 1.05

    C[np.arange(M, M + N), np.arange(N)] = np.ones(N) * track_end_cost
    C[np.arange(M), np.arange(N, N + M)] = np.ones(M) * track_start_cost
    min_val = np.min(C.data) if len(C.data) > 0 else 0
    C[dist_matrix.col + M, dist_matrix.row + N] = min_val

    return C.to_coo_matrix()


def build_segment_cost_matrix(
    gap_closing_dist_matrix: Union[coo_matrix_builder, Matrix],
    splitting_dist_matrix: Union[coo_matrix_builder, Matrix],
    merging_dist_matrix: Union[coo_matrix_builder, Matrix],
    track_start_cost: Optional[Float],
    track_end_cost: Optional[Float],
    no_splitting_cost: Optional[Float],
    no_merging_cost: Optional[Float],
    alternative_cost_factor: Float = 1.05,
    alternative_cost_percentile: Float = 90,
    alternative_cost_percentile_interpolation: str = "lower",
) -> coo_matrix:
    """Build sparce array for segment-linking cost matrix.

    Parameters
    ----------
    gap_closing_dist_matrix : coo_matrix_builder or Matrix
        The distance matrix for closing gaps between segment i and j.
    splitting_dist_matrix : coo_matrix_builder or Matrix
        The distance matrix for splitting between segment i and time/index j
    merging_dist_matrix : coo_matrix_builder or Matrix
        The distance matrix for merging between segment i and time/index j
    track_start_cost : Float, optional
        The cost for starting the track (b in Jaqaman et al 2008 NMeth)
    track_end_cost : Float, optional
        The cost for ending the track (d in Jaqaman et al 2008 NMeth)
    no_splitting_cost : Float, optional
        The cost to reject splitting (d' in Jaqaman et al 2008 NMeth)
    no_merging_cost : Float, optional
        The cost to reject merging (b' in Jaqaman et al 2008 NMeth)
    alternative_cost_factor: Float
        The factor to calculate the alternative costs, by default 1.05.
    alternative_cost_percentile: Float
        The percentile to calculate the alternative costs, by default 90.
    alternative_cost_percentile_interpolation: str
        The percentile interpolation to calculate the alternative costs,
        by default "lower".
        See `numpy.percentile` for allowed values.

    Returns
    -------
    cost_matrix : Optional[coo_matrix]
        the cost matrix for frame linking, None if not appropriate
    """
    M = gap_closing_dist_matrix.shape[0]
    assert gap_closing_dist_matrix.shape[1] == M
    assert splitting_dist_matrix.shape[0] == M
    assert merging_dist_matrix.shape[0] == M
    N1 = splitting_dist_matrix.shape[1]
    N2 = merging_dist_matrix.shape[1]

    S = 2 * M + N1 + N2

    C = coo_matrix_builder((S, S), dtype=np.float32)

    C.append_matrix(gap_closing_dist_matrix)
    C.append_matrix(splitting_dist_matrix.T, shift=(M, 0))
    C.append_matrix(merging_dist_matrix, shift=(0, M))

    upper_left_size = C.size()
    if upper_left_size == 0:
        return None

    # Note:
    # Though the way of assigning track_start_cost, track_end_cost, no_splitting_cost, no_merging_cost # noqa :
    # and min_val is similar to that of TrackMate (link1, link2), GPL3 of TrackMate does not apply. (See link3 for license discussion.) # noqa :
    #   link1 https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/costmatrix/DefaultCostMatrixCreator.java#L186 # noqa :
    #         https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/costmatrix/JaqamanSegmentCostMatrixCreator.java # noqa:
    #         https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/SparseLAPSegmentTracker.java#L148 # noqa:
    #   link2 (default parameters for alternative_cost_percentile, alternative_cost_factor) # noqa :
    #         https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/TrackerKeys.java # noqa :
    #   link3 https://forum.image.sc/t/linear-assignment-problem-based-tracking-package-in-python/57793 # noqa :
    #         https://web.archive.org/web/20210921134401/https://forum.image.sc/t/linear-assignment-problem-based-tracking-package-in-python/57793 # noqa :

    if (
        track_start_cost is None
        or track_end_cost is None
        or no_splitting_cost is None
        or no_merging_cost is None
    ):
        alternative_cost = (
            np.percentile(
                C.data,
                alternative_cost_percentile,
                interpolation=alternative_cost_percentile_interpolation,
            )
            * alternative_cost_factor
        )
        if track_start_cost is None:
            track_start_cost = alternative_cost
        if track_end_cost is None:
            track_end_cost = alternative_cost
        if no_splitting_cost is None:
            no_splitting_cost = alternative_cost
        if no_merging_cost is None:
            no_merging_cost = alternative_cost

    C[np.arange(M + N1, 2 * M + N1), np.arange(M)] = np.ones(M) * track_start_cost
    C[np.arange(2 * M + N1, S), np.arange(M, M + N2)] = np.ones(N2) * no_merging_cost
    C[np.arange(M), np.arange(M + N2, 2 * M + N2)] = np.ones(M) * track_end_cost
    C[np.arange(M, M + N1), np.arange(2 * M + N2, S)] = np.ones(N1) * no_splitting_cost
    min_val = np.min(
        [track_start_cost, track_end_cost, no_splitting_cost, no_merging_cost]
    )

    upper_left_rows = C.row[:upper_left_size]
    upper_left_cols = C.col[:upper_left_size]
    C[upper_left_cols + M + N1, upper_left_rows + M + N2] = min_val

    return C.to_coo_matrix()

Build sparce array for frame-linking cost matrix.      Parameters     ----------     dist_matrix : Matrix or `_utils.coo_matrix_builder`         The distance matrix for points at time t and t+1.     track_start_cost : Float, optional         The cost for starting the track (b in Jaqaman et al 2008 NMeth)     track_end_cost : Float, optional         The cost for ending the track (d in Jaqaman et al 2008 NMeth)      Returns     -------     cost_matrix : FloatArray         the cost matrix for frame linking Build sparce array for segment-linking cost matrix.      Parameters     ----------     gap_closing_dist_matrix : coo_matrix_builder or Matrix         The distance matrix for closing gaps between segment i and j.     splitting_dist_matrix : coo_matrix_builder or Matrix         The distance matrix for splitting between segment i and time/index j     merging_dist_matrix : coo_matrix_builder or Matrix         The distance matrix for merging between segment i and time/index j     track_start_cost : Float, optional         The cost for starting the track (b in Jaqaman et al 2008 NMeth)     track_end_cost : Float, optional         The cost for ending the track (d in Jaqaman et al 2008 NMeth)     no_splitting_cost : Float, optional         The cost to reject splitting (d' in Jaqaman et al 2008 NMeth)     no_merging_cost : Float, optional         The cost to reject merging (b' in Jaqaman et al 2008 NMeth)     alternative_cost_factor: Float         The factor to calculate the alternative costs, by default 1.05.     alternative_cost_percentile: Float         The percentile to calculate the alternative costs, by default 90.     alternative_cost_percentile_interpolation: str         The percentile interpolation to calculate the alternative costs,         by default "lower".         See `numpy.percentile` for allowed values.      Returns     -------     cost_matrix : Optional[coo_matrix]         the cost matrix for frame linking, None if not appropriate # Note: # Though the way of assigning track_start_cost, track_end_cost, no_splitting_cost, no_merging_cost # noqa : # and min_val is similar to that of TrackMate (link1, link2), GPL3 of TrackMate does not apply. (See link3 for license discussion.) # noqa : #   link1 https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/costmatrix/DefaultCostMatrixCreator.java#L186 # noqa : #         https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/costmatrix/JaqamanSegmentCostMatrixCreator.java # noqa: #         https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/sparselap/SparseLAPSegmentTracker.java#L148 # noqa: #   link2 (default parameters for alternative_cost_percentile, alternative_cost_factor) # noqa : #         https://github.com/fiji/TrackMate/blob/5a97426586b3c592c986c57aa1a09bab9d21419c/src/main/java/fiji/plugin/trackmate/tracking/TrackerKeys.java # noqa : #   link3 https://forum.image.sc/t/linear-assignment-problem-based-tracking-package-in-python/57793 # noqa : #         https://web.archive.org/web/20210921134401/https://forum.image.sc/t/linear-assignment-problem-based-tracking-package-in-python/57793 # noqa :