cscorr {gdi}

Measure and analyze cross-sectional geometry supplied as an image.

Description

Measure and analyze cross-sectional geometry supplied as an image.

Usage

cscorr(
  image_file,
  threshold = 0.5,
  channel = 4,
  method = "greater",
  return = "area_corr",
  k = 2,
  scale = 1
)

Arguments

image_file

Image to be read. Images can be jpeg or png files, or a previously read image saved as an array/matrix-type object in R.

threshold

Reference value for color criterium after which pixels that are part of the cross-section are differentiated from the background.

channel

Color channel to which to apply the threshold criterium. Default is 4 (alpha channel of rgba image). Channel setting needs to be adjusted depending on the color mode of the image used (e.g. there are two channels to choose from in a greyscale image, and 3 in an rgb image).

method

Method for determining which pixels to count. Default "greater" counts pixels with value greater than threshold (e.g. higher opacity, in the case of an alpha channel). "less" counts pixels with a value less than the threshold. "not" counts all pixels not precisely matching threshold. Any other character string results in only pixels exactly matching the value given as threshold being counted.

return

What value to return. Possible values are "area_corr" (Default, returns ratio between measured area and area of ellipse with same horizontal and vertical diameters), "aspect_ratio" (returns aspect ratio), "diameters" (returns diameters), "area" (returns area) and "rotI" (returns correction factors for rotational inertia calculations). Any other value for this parameter will prompt the function to return a vector containing all of these outputs.

k

optional superellipse exponent for the (super)ellipse to which the measurements should be compared (for the "area_corr" setting for the parameter return).

scale

Optional scale of the image (for raw area measurements).

Value

Either a numeric of length 1 (depending on the input of the return parameter), defaulting to the area correction factor (if return=="area_corr"), or (if return is left empty or does not match any of the predefined settings) a numeric vector with 8 elements, containing all the possible outputs (x and y diameters, aspect ratio, area and area correction factor, correction factors representing ratios of rotational inertia in x, y and z planes relative an ellipse of equal diameters).

Examples

fdir <- system.file(package="gdi")
correction_factor <- cscorr(file.path(fdir,"exdata","cross_section.png"))