shapeR (version 1.0-1)

write.image.with.outline: Write outlines on top of the original images for quality checking

Description

A function which writes the outlines which were extracted from the images in the folder "Fixed" on top of the corresponding images in the "Original" folder. Viewing the resulted images in the folder "Original_with_outlines" is a good quality check to ensure the correct outline has been extracted. If the outline is not correct, then the image can be fixed in an image software, such as GIMP (www.gimp.org), placed in the "Fixed" folder and then the detect.outline step is repeated. The function detect.outline calls this function if the parameter write.outline.w.org is set to TRUE.

Usage

write.image.with.outline(object, folder = NA, fname = NA, doProgress = TRUE)

Value

None

Arguments

object

A shapeR object

folder

The folder name where the image is stored

fname

Image file name. Not including the extension ".jpg"

doProgress

If TRUE, a progressbar is shown

Author

Lisa Anne Libungan

References

Libungan LA and Palsson S (2015) ShapeR: An R Package to Study Otolith Shape Variation among Fish Populations. PLoS ONE 10(3): e0121102. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121102

Examples

if (FALSE) {
#Use test data from Libungan and Palsson (2015) and run the following lines:
shape = shapeR("ShapeAnalysis/","FISH.csv")
shape = detect.outline(shape,write.outline.w.org = FALSE)
write.image.with.outline(shape)}