find_blobs {Bioi}

Assign all neighboring pixels the same group number.

Description

Perform connected-component labeling to group continuous, thresholded objects in 3-dimensional arrays.

This function takes a vector, matrix, or 3-dimensional array where each element is TRUE if it corresponds to an object-positive index or FALSE if it corresponds to a background index. An object of the same dimension as the input is returned. All connected object indices take the value of their group number and all background indices take the value NA.

Usage

find_blobs(
  arr,
  use_prog_bar = TRUE,
  run_parallel = FALSE,
  num_cores = NULL,
  partition_req = NULL,
  parallel_call_depth = 3
)

Arguments

arr

A vector, matrix, or 3-dimensional array where object-positive elements are denoted by the value TRUE and background elements are denoted by the value FALSE.

use_prog_bar

TRUE/FALSE indicating whether a progress bar should be used. This is only available when run_parallel is FALSE.

run_parallel

TRUE/FALSE indicating whether operations should be performed in parallel. This is only valid if partitioning is performed.

num_cores

The number of cores to use if running in parallel.

partition_req

The minimum number of points required to create a new partition.

parallel_call_depth

The number of levels of partitioning that should be performed before terminating calls to run operations in parallel. The number of threads opened when running in parallel is equal to 2^(parallel_call_depth)*num_cores.

Author(s)

Zach Colburn

Examples

# Generate a random matrix.
set.seed(10)
mat <- matrix(runif(70), nrow = 7)

# Arbitrarily say that everything below 0.8 is background.
logical_mat <- mat > 0.8

# Find blobs.
find_blobs(logical_mat)