Execute the OTB command list via system call

Wrapper function which paste the OTB command list into a system call compatible string and execute this command.

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

Arguments

otbCmdList

the OTB algorithm parameter list

gili

optional list providing the linkage to OTB as done by `linkOTB()`. If not provided the `runOTB` function try to link automatically.

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 codewort ($input_in or $input_il).

Examples

if (FALSE) {
require(link2GI)
require(terra)
require(listviewer)

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

if (otblink$exist) {
 projRootDir<-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)
 
}
}