runOTB function

Execute the OTB command via system call

Wrapper function that inserts the OTB command list into a system call compatible string and executes that command.

runOTB(
  otbCmdList = NULL,
  gili = NULL,
  retRaster = TRUE,
  retCommand = FALSE,
  quiet = TRUE
)

Arguments

• otbCmdList: the correctly populated OTB algorithm parameter list
• gili: optional list of available OTB installations, if not specified, linkOTB() is called to automatically try to find a valid OTB installation
• retRaster: boolean if TRUE a raster stack is returned default is FALSE
• retCommand: boolean if TRUE only the OTB API command is returned default is FALSE
• quiet: boolean if TRUE suppressing messages default is TRUE

Details

#' Please NOTE: You must check the help to identify the correct input file argument ($input_in or$input_il).

Examples

## Not run:

require(link2GI)
require(terra)
require(listviewer)

## link to OTB
otblink<-link2GI::linkOTB()

if (otblink$exist) {
 root_folder<-tempdir()
 fn <- system.file('ex/elev.tif', package = 'terra')

## for an image output example we use the Statistic Extraction, 
algoKeyword<- 'LocalStatisticExtraction'

## extract the command list for the choosen algorithm 
cmd<-parseOTBFunction(algo = algoKeyword, gili = otblink)

## Please NOTE:
## You must check the help to identify the correct argument codewort ($input_in or $input_il)
listviewer::jsonedit(cmd$help)

## define the mandatory arguments all other will be default
cmd$input_in  <- fn
cmd$out <- file.path(tempdir(),'test_otb_stat.tif')
cmd$radius <- 7

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

## plot image
terra::plot(retStack)

## for a data output example we use the 

algoKeyword<- 'ComputeImagesStatistics'

## extract the command list for the chosen algorithm 
cmd<-parseOTBFunction(algo = algoKeyword, gili = otblink)

## get help using the convenient listviewer
listviewer::jsonedit(cmd$help)

## define the mandatory arguments all other will be default
cmd$input_il  <- file.path(tempdir(),'test.tif')
cmd$ram <- 4096
cmd$out.xml <- file.path(tempdir(),'test_otb_stat.xml')
cmd$progress <- 1

## run algorithm
ret <- runOTB(cmd,gili = otblink, quiet = F)

## as vector
print(ret)

## as xml
XML::xmlParse(cmd$out)
 
}
## End(Not run)