sbatch

Sbatch executable setup

require(jsonlite, lib.loc = "/scratch/vljchr004/")


args = commandArgs(TRUE)
dirX = args[1]
input2 = args[2]

if(!file.exists(dirX)|!file.exists(input2)){
   cat('Cannot find', input_path, 'exiting!\n')
   stop()
}


require(keras, lib.loc = "/scratch/vljchr004/")

Json wrangling (non-hardcoded)

#test

dirX="/Users/gerhard/msc-thesis-data/gridtest"

wrangle <- function(dirX){
  
  require(jsonlite)
  
  files <- list.files(path=paste0(dirX),
                      pattern="*json",
                      full.names=T,
                      recursive=TRUE)
  
  j <- fromJSON(files[1])
  
  print("---------------------------------------------------------------------------------")
  print(paste0("Processing jsons to list:"))
  
  for(i in 2:length(files)){
    print(100*(i/length(files)))
    
    f <- fromJSON(files[i])
    j <- c(j,f)
  }
  
  j
  
}

dat <- wrangle(dirX)

## Loading required package: jsonlite

## [1] "---------------------------------------------------------------------------------"
## [1] "Processing jsons to list:"
## [1] 50
## [1] 75
## [1] 100

print("---------------------------------------------------------------------------------")

## [1] "---------------------------------------------------------------------------------"

print("DONE")

## [1] "DONE"

print("---------------------------------------------------------------------------------")

## [1] "---------------------------------------------------------------------------------"

print("Extracting layers and momenta...")

## [1] "Extracting layers and momenta..."

p <- sapply(dat,`[[`,"P")
pdg <- sapply(dat, `[[`,"pdgCode")
layer_0 <- sapply(dat, `[[`,"layer 0")
layer_1 <- sapply(dat, `[[`,"layer 1")
layer_2 <- sapply(dat, `[[`,"layer 2")
layer_3 <- sapply(dat, `[[`,"layer 3")
layer_4 <- sapply(dat, `[[`,"layer 4")
layer_5 <- sapply(dat, `[[`,"layer 5")

print("---------------------------------------------------------------------------------")

## [1] "---------------------------------------------------------------------------------"

print("Removing NULLS")

## [1] "Removing NULLS"

n <- unique(
  c(
  which(sapply(layer_0, is.null)),
  which(sapply(layer_1, is.null)),
  which(sapply(layer_2, is.null)),
  which(sapply(layer_3, is.null)),
  which(sapply(layer_4, is.null)),
  which(sapply(layer_5, is.null))
  )
  )

pdg <- pdg[-n]

layer_0 <- layer_0[-n]

layer_1 <- layer_1[-n]

layer_2 <- layer_2[-n]

layer_3 <- layer_3[-n]

layer_4 <- layer_4[-n]

layer_5 <- layer_5[-n]

p <- p[-n]

print("---------------------------------------------------------------------------------")

## [1] "---------------------------------------------------------------------------------"

print("Removing empties:")

## [1] "Removing empties:"

e <- unique(
  
  as.numeric(which(sapply(layer_0, "typeof")=="list")),
  as.numeric(which(sapply(layer_1, "typeof")=="list")),
  as.numeric(which(sapply(layer_2, "typeof")=="list")),
  as.numeric(which(sapply(layer_3, "typeof")=="list")),
  as.numeric(which(sapply(layer_4, "typeof")=="list")),
  as.numeric(which(sapply(layer_5, "typeof")=="list"))
  
)

pdg <- pdg[-e]

layer_0 <- layer_0[-e]

layer_1 <- layer_1[-e]

layer_2 <- layer_2[-e]

layer_3 <- layer_3[-e]

layer_4 <- layer_4[-e]

layer_5 <- layer_5[-e]

p <- p[-e]