forImage (version 0.1.0)

measure: Foraminifera image measurement

Description

This function measures dimensions in photomicrographs.

Usage

measure(file, scale = NULL, ref_scale = NULL,
unit = "um", pco = FALSE, save = FALSE, path = NULL)

Arguments

file

image file with or without metadata.

scale

(optional) image physical pixel size (metric / pixel).

ref_scale

(optional) reference scale available on image (in micrometers or millimeters). This scale should be inserted under the main object.

unit

scale unit. Needs to agree with reference scale or metric per pixel. (Default "um")

pco

(optional) will assess proportion of cell occupancy inside the shell. Outlined proportion. This argument is still being tested and should be used with caution.

save

If TRUE save the result image in a specified folder (see path) or the working directory, if FALSE it does not save the image with measures. (Default FALSE)

path

(optional) path to save result file.

Value

A `data.frame` containing the file name, surface area and major and minor axis. The unit is dependent on the pixel per metric scale. It also returns a PNG file with the measured dimensions if save = TRUE.

See Also

bio.volume, volume.total

Examples

# NOT RUN {
#Path to example file from package
img <- system.file("extdata", "foram.tif", package="forImage")

#measure individual dimension
measure(img)
# }
# NOT RUN {
# }