A typical usecase for the Orfeo Toolbox wrapper

link2GI supports the use of the Orfeo Toolbox with a listbased simple wrapper function. Actually two functions parse the modules and functions syntax dumps and generate a command list that is easy to modify 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 choose 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()
 projRootDir<-tempdir()

data('rgb', package = 'link2GI')  
raster::plotRGB(rgb)
r<-raster::writeRaster(rgb, 
              filename=file.path(projRootDir,"test.tif"),
              format="GTiff", overwrite=TRUE)
## 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$input  <- file.path(projRootDir,"test.tif")
cmd$filter <- "touzi"
cmd$channel <- 2
cmd$out <- file.path(projRootDir,paste0("out",cmd$filter,".tif"))

## run algorithm
retStack<-runOTB(cmd,gili = otblink)

## plot filter raster on the green channel
plot(retStack)