measure {forImage} | R Documentation |
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 |
(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
.
Author(s)
Thaise R. Freitas thaisericardo.freitas@gmail.com
See Also
Examples
## Not run:
#Path to example file from package
img <- system.file("extdata", "foram.tif", package="forImage")
#measure individual dimension
measure(img)
## End(Not run)