Function poisson_equation has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

def poisson_equation(
    image, gradient=1, max_iter=100, convergence=0.01, percentile=90.0
):
    """Estimate the solution to the Poisson Equation

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Function ellipse_from_second_moments_ijv has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

def ellipse_from_second_moments_ijv(
    i, j, image, labels, indexes, wants_compactness=False
):
    """Calculate measurements of ellipses equivalent to the second moments of labels
    

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Function calculate_costs has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def calculate_costs(self, detections_1, detections_2, calculate_match_cost, params):
        """
        Calculates assignment costs between detections and 'empty' spaces. The smaller cost the better.

        @param detections_1: cell list of size n in previous frame

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Function feret_diameter has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

def feret_diameter(chulls, counts, indexes):
    """Return the minimum and maximum Feret diameter for each object
    
    This function takes the convex hull data, as generated by convex_hull
    and returns the minimum and maximum Feret diameter for each convex hull.

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Function bg_compensate has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

def bg_compensate(img, sigma, splinepoints, scale):
    """Reads file, subtracts background. Returns [compensated image, background]."""

    from PIL import Image
    import pylab

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Function get_robust_background_threshold has 7 arguments (exceeds 4 allowed). Consider refactoring.

Open

def get_robust_background_threshold(

Function __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def __init__(

Function ellipse_from_second_moments_ijv has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

def ellipse_from_second_moments_ijv(

Avoid deeply nested control flow statements.

Open

                        if h == umin:
                            if y[j1] == n:
                                raise StopIteration()
                            print("Add to scan")
                            scan += [j1]

Avoid deeply nested control flow statements.

Open

                    if neighbor_value < current_value:
                        mask_value = values[neighbor + image_stride]
                        # Only do neighbors less than the mask value
                        if neighbor_value < mask_value:
                            # Raise the neighbor to the mask value if

Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def __init__(self, image, labels, scale_i, scale_j, nlevels=8, mask=None):

Function entropy has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def entropy(data, bins=256):
    """Compute a threshold using Ray's entropy measurement
    
    data           - an array of intensity values between zero and one
    bins           - we bin the data into this many equally-spaced bins, then pick

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Function find_visible has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def find_visible(hull, observer, background):
    """Given an observer location, find the first and last visible
       points in the hull
       
       The observer at "observer" is looking at the hull whose most distant

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Function label_skeleton has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def label_skeleton(skeleton):
    """Label a skeleton so that each edge has a unique label
    
    This operation produces a labels matrix where each edge between
    two branchpoints has a different label. If the skeleton has been

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Avoid deeply nested control flow statements.

Open

                    for adjacent_i, adjacent_j in (
                        (ii - 1, jj),
                        (ii, jj - 1),
                        (ii + 1, jj),
                        (ii, jj + 1),

Function binary_shrink has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def binary_shrink(image, iterations=-1):
    """Shrink an image by repeatedly removing pixels which have partners
       above, to the left, to the right and below until the image doesn't change
       
       image - binary image to be manipulated

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Function lines_intersect has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def lines_intersect(pt1_p, pt2_p, pt1_q, pt2_q):
    """Return true if two line segments intersect
    pt1_p, pt2_p - endpoints of first line segment
    pt1_q, pt2_q - endpoints of second line segment
    """

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Function bilateral_filter has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

def bilateral_filter(

Avoid deeply nested control flow statements.

Open

                    if neighbor < 0:
                        raise IndexError(
                            "Index out of bounds: %d, current=%d, current_value=%d"
                            % (neighbor, np.unravel_index(current, dims), current_value)
                        )

Function splinefit2d has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

def splinefit2d(x, y, z, px, py, mask=None):