old_C_code/stage1/wrapper.R

   1 ppam_exe = function(path=".", np=parallel::detectCores(), data=NULL,
   2     args="DontLetMeEmptyPlease!")
   3 {
   4     command_line = paste("mpirun -np ",np," ",path,"/ppam.exe cluster",sep="")
   5
   6     #if data provided (as data.frame or matrix...): binarize it, and add it as first argument
   7     if (!is.null(data))
   8     {
   9         if (!is.character(data))
  10         {
  11             #assuming matrix or data.frame, WITH row names
  12             #( identifiers; could be line number... e.g. data <- cbind(1:nrow(data),data) )
  13             write.table(data, "/tmp/data_csv", sep=",", row.names=FALSE, col.names=FALSE)
  14             system(paste(path,"/ppam.exe serialize /tmp/data_csv /tmp/data_bin 0 0",sep=""))
  15         } else
  16         {
  17             system(paste(path,"/ppam.exe serialize ",data," /tmp/data_bin 0 0",sep=""))
  18         }
  19         command_line = paste(command_line," /tmp/data_bin",sep="")
  20     }
  21
  22     command_line = paste(command_line," ",args,sep="")
  23     system(command_line)
  24 }
  25
  26 #NOTE: identifiers in first column
  27 getMedoids = function(path=".", xmlResult = "ppamResult.xml",
  28     finalSeries = "ppamFinalSeries.bin")
  29 {
  30     system(paste(path,"/ppam.exe deserialize ",finalSeries," ppamFinalSeries.csv -1",sep=""))
  31     curves = read.table("ppamFinalSeries.csv", sep=",")
  32     library(XML)
  33     ranks = as.integer( xmlToList( xmlParse(xmlResult) )$ranks )
  34     return ( curves[ranks,] ) # == medoids
  35 }
  36
  37 getDistor = function(path=".", xmlResult = "ppamResult.xml",
  38     finalSeries = "ppamFinalSeries.bin")
  39 {
  40     system(paste(path,"/ppam.exe classif ",finalSeries," ",xmlResult,sep=""))
  41 }
  42
  43 serialize = function(path=".", csvSeries, binSeries, byCols=0, nbSeries=0)
  44 {
  45     system(paste(path,"/ppam.exe serialize ",csvSeries," ",binSeries," ",byCols," ",nbSeries,
  46         sep=""))
  47 }
  48
  49 deserialize = function(path=".", binSeries, csvSeries, ranks="-1")
  50 {
  51     system(paste(path,"/ppam.exe deserialize ",binSeries," ",csvSeries," ",ranks,sep=""))
  52     return ( read.table(csvSeries, sep=",") )
  53 }