link2GI supports the use of the Orfeo Toolbox with a simple list-based wrapper function. Actually, two functions parse the module and function syntax dumps and generate a command list that can be easily modified with the necessary arguments.
Usually you have to get the module list first:
# link to the installed OTB
otblink<-link2GI::linkOTB()
# get the list of modules from the linked version
algo<-parseOTBAlgorithms(gili = otblink)Based on the modules of the current version of `OTB’, you can then select the module(s) you want to use.
## for the example we use the edge detection,
algoKeyword<- "EdgeExtraction"
## extract the command list for the choosen algorithm
cmd<-parseOTBFunction(algo = algoKeyword, gili = otblink)
## print the current command
print(cmd)Admittedly this is a very straightforward and preliminary approach.
Nevertheless it provids you a valid list of all OTB API
calls that can easily manipulated for your needs. The following working
example will give you an idea how to use it.
require(link2GI)
require(raster)
require(listviewer)
otblink<-link2GI::linkOTB()
root_dir<-tempdir()
fn <- system.file("ex/elev.tif", package = "terra")
## for the example we use the edge detection,
algoKeyword<- "EdgeExtraction"
## extract the command list for the choosen algorithm
cmd<-parseOTBFunction(algo = algoKeyword, gili = otblink)
## get help using the convenient listviewer
listviewer::jsonedit(cmd$help)
## define the mandantory arguments all other will be default
cmd$input_in <- fn
cmd$filter <- "touzi"
cmd$channel <- 1
cmd$out <- paste0(root_dir,paste0("\\out",cmd$filter,".tif"))
## run algorithm
retStack<-runOTB(cmd,gili = otblink)
## plot filter raster on the green channel
plot(retStack)