roi2polygon: Convert a roi object (from ImageJ program) to an object of...

Usage Arguments Examples

Usage

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roi2polygon(roi.path, tif.path)

Arguments

roi.path
tif.path

Examples

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##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (roi.path, tif.path) 
{
    library(RImageJROI)
    roi.file.names <- roi.path
    x_roi5 <- read.ijroi(roi.file.names, verbose = FALSE)
    library(spatstat)
    x_owin5 <- ij2spatstat(x_roi5)
    first.tif.filename <- Sys.glob(paste0(tif.path, "vis/*.tif"))[[1]]
    library(raster)
    RGB_stack_DEM <- stack(first.tif.filename)
    bandred <- raster(first.tif.filename, band = 1)
    w5_y_corr <- (nrow(as.matrix(bandred)) - (as.data.frame(x_owin5))$y)/nrow(RGB_stack_DEM)
    w5_x <- (as.data.frame(x_owin5))$x/ncol(RGB_stack_DEM)
    xym5 <- cbind(x = w5_x, y = w5_y_corr)
    p5 <- Polygon(xym5)
    ps5 <- Polygons(list(p5), "pocillo 5")
    sps <- SpatialPolygons(list(ps5))
    return(sps)
  }

united-ecology/photomoss documentation built on May 14, 2019, 2:30 p.m.