runOTB: Execute the OTB command via system call

In link2GI: Linking Geographic Information Systems, Remote Sensing and Other Command Line Tools

Execute the OTB command via system call

Description

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

Usage

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)

link2GI documentation built on Oct. 28, 2024, 5:06 p.m.