convertROI {phenopix}

Convert a region of interest object from the old structure to the new (phenopix > 2.4)

Description

This function allows to convert the roi.data stored in the roi.data.Rdata object built with phenopix older than version 2.4 into the new structure better described in the details section. The changed was needed because a new method for drawing a region of interest was conceived, which includes the possibility to draw multiple polygons for a single ROI. The new function that does the job is DrawMULTIROI, which fully substitutes the old DrawROI.

Usage

convertROI(path_img_ref, path_ROIs, file.type='.jpg')

Arguments

path_img_ref

Path in your folder for the reference image

path_ROIs

Path where roi.data object created with phenopix < 2.4 was built.

file.type

It must match the syntax of your file extension (e.g. .jpg, .JPG, .JPEG). Multiple types are allowed by concatenation with c().

Details

This function allows to convert the roi.data stored in the roi.data.Rdata object built with phenopix older than version 2.4 into the new structure better described in the details section. The changed was needed because a new method for drawing a region of interest was conceived, which includes the possibility of drawing multiple polygons for a single ROI. There is a second reason why DrawROI had to disappear: it included C++ code from the package SDMTools which is currently orphaned. The new function that allows multiple polygons in a single ROI is DrawMULTIROI, which fully substitutes the old DrawROI.

Value

A list containing the following:

mask

A binary mask (a raster object)

polygons

An object of class SpatialPolygons

Additionally, a jpeg image is returned with the ROI(s) drawn. The same object that is returned is saved in the path specified in path_ROIs

Author(s)

Gianluca Filippa <[e-mail]>