extract_pheno: Extract phenotypical features from segmented images

In rwang14/implant: A High-throughput Phenotyping Pipeline for Image Processing and Functional Growth Curve Analysis

Description

This function extracts phenotypical features from segmented images.

Usage

extract_pheno(processed_image, Xsize = 1, Ysize = 1, a = 1, b = 1)

Arguments

processed_image	a binary matrix contains only 0 and 1, giving the segmented image of a plant.
Xsize, Ysize	Xsize and Ysize are the actual horizontal and vertical lengths of one pixel, respectively. The default set is Xsize = 1, Ysize = 1 for the non-adjustment for the pixel size.
a,b	positive integers, the same as the values of RowSample and ColSample in the function: "downsize", respectively. This is only used if the function "downsize" was used to reduce the size of the image in image segmentation.

Value

pixelCount	The total number of pixels of the segmented plant of interest.
plantheight	The height of the segmented plant.
plantwidth	The width of the segmented plant.
plantSize	The size of the segmented plant based on the total number of pixels of the segmented plant of interest. i.e. Size = pixelCount * Xsize * Ysize.

See Also

downsize for reducing size of an image.

Examples

#read an RGB image
library(png)
imageOriginal = readPNG(system.file("extdata", "image1.png",
                             package = "implant",
                             mustWork = TRUE))[ , ,c(1:3)]
#reduce the size of an image
image_reduced = downsize(imageOriginal, RowSample = 2, ColSample = 2)
#segment the reduced image
imageB = imageBinary(image_reduced,  weight = c(-1, 2, -1), threshold1 = 30 / 255, threshold2 = 0.05)
#obtain the size of the segmented image
extract_pheno(processed_image = imageB, Xsize = 1.5, Ysize = 1.5, a = 2, b = 2)$size

rwang14/implant documentation built on Sept. 6, 2020, 3:21 a.m.