fillLineGaps {biopixR}

Reconnecting discontinuous lines

Description

The function attempts to fill in edge discontinuities in order to enable normal labeling and edge detection.

Usage

fillLineGaps(
  contours,
  objects = NULL,
  threshold = "13%",
  alpha = 1,
  sigma = 2,
  radius = 5,
  iterations = 2,
  visualize = TRUE
)

Arguments

contours

image that contains discontinuous lines like edges or contours

objects

image that contains objects that should be removed before applying the fill algorithm

threshold

"in %" (from threshold)

alpha

threshold adjustment factor for edge detection (from edgeDetection)

sigma

smoothing (from edgeDetection)

radius

maximal radius that should be scanned for another cluster

iterations

how many times the algorithm should find line ends and reconnect them to their closest neighbor

visualize

if TRUE (default) a plot is displayed highlighting the added pixels in the original image

Details

The function pre-processes the image in order to enable the implementation of the adaptiveInterpolation function. The pre-processing stage encompasses a number of operations, including thresholding, the optional removal of objects, the detection of line ends and diagonal line ends, and the labeling of pixels. The threshold should be set to allow for the retention of some "bridge" pixels between gaps, thus facilitating the subsequent process of reconnection. For further details regarding the process of reconnection, please refer to the documentation on adaptiveInterpolation. The subsequent post-processing stage entails the reduction of line thickness in the image. With regard to the possibility of object removal, the coordinates associated with these objects are collected using the objectDetection function. Subsequently, the pixels of the detected objects are set to null in the original image, thus allowing the algorithm to proceed without the objects.

Value

Image with continuous edges (closed gaps).

Examples

fillLineGaps(droplets)