RootscanR (version 0.0.1)

skelPxWidth: Count skeleton root pixels with certain widths in the base root image

Description

skelPxWidth - Counts the skeleton pixels that belong to root pieces of certain (circular) widths (diameter <3px, 3-7px, >7px).
For each white root pixel in the skeleton image, it checks how large (in terms of the categories <3px, 3-7px, >7px, which equal a radius of <1px, 1-3px, >=4px) the circle of white root pixels is that surrounds it in the base root image.
Optionally, a masking layer can be specified that indicates which pixels of the skeleton image should be checked (the radius of the white circle is still check in the complete base image).

Usage

skelPxWidth(base_img, skel_img, mask = NULL)

Value

skelPxWidth Numeric vector of length 3 containing the counts.

Arguments

base_img

Base image (provided by the RootDetector). Can be a PNG, i.e., an array with 3 dimensions (3 layers each containing a 2-dim. numeric matrix with values between 0 and 1), or a 2-dim. matrix.

skel_img

Skeleton image with the same number of rows and columns as base_img (provided by the RootDetector). Can be a PNG, i.e., an array with 3 dimensions (3 layers each containing a 2-dim. numeric matrix with values between 0 and 1), or a 2-dim. matrix.

mask

2-dim. true/false-matrix with the same number of rows and columns as base_img (optional, default = NULL, interpreted as a matrix consisting only of TRUEs, i.e., nothing is "removed" from the image).

Examples

# In this example there are 2 white root pixels in the skeleton image.
# The left one is completely surrounded by white pixels in the base image,
# it falls into Category 2 (3-7px). The bottom right one has a black
# neighboring pixel and thus falls in to Category 1 (<3px). Thus, the result
# is Categorie 1: 1 pixel, Cat. 2: 1 pixel, Cat. 3: 0 pixels.
skelPxWidth(base_img = matrix(c(1,1,1,0,
                     1,1,1,0,
                     1,1,1,1), ncol = 4, nrow = 3, byrow = TRUE),
            skel_img = matrix(c(0,0,0,0,
                     0,1,0,0,
                     0,0,0,1), ncol = 4, nrow = 3, byrow = TRUE))
# Similar example with a mask which makes the function "ignore" the right
# side of the skeleton image.
# The function still identifies the left white pixel as of Category 2.
skelPxWidth(matrix(c(1,1,1,0,
                     1,1,1,0,
                     1,1,1,1), ncol = 4, nrow = 3, byrow = TRUE),
            matrix(c(0,0,0,0,
                     0,1,0,0,
                     0,0,0,1), ncol = 4, nrow = 3, byrow = TRUE),
             matrix(c(TRUE,TRUE,FALSE,FALSE,
                      TRUE,TRUE,FALSE,FALSE,
                      TRUE,TRUE,FALSE,FALSE), ncol = 4, nrow = 3,
                      byrow = TRUE))