old_C_code/wrapper.R

   1 ppam_exe = function(path=".", np=parallel::detectCores(), data=NULL,
   2     nbSeriesPerChunk, nbClusters, randomize=1, p_dissims=2)
   3 {
   4     args = paste(nbSeriesPerChunk," ",nbClusters," ",randomize," ",p_dissims,sep="")
   5
   6     command_line = paste("mpirun -np ",np," ",path,"/ppam.exe cluster",sep="")
   7
   8     #if data provided (as data.frame or matrix...): binarize it, and add it as first argument
   9     if (!is.null(data))
  10     {
  11         if (!is.character(data))
  12         {
  13             #assuming matrix or data.frame, WITH row names
  14             #( identifiers; could be line number... e.g. data <- cbind(1:nrow(data),data) )
  15             write.table(data, "/tmp/data_csv", sep=",", row.names=FALSE, col.names=FALSE)
  16             system(paste(path,"/ppam.exe serialize /tmp/data_csv /tmp/data_bin 0 0",sep=""))
  17         } else
  18         {
  19             system(paste(path,"/ppam.exe serialize ",data," /tmp/data_bin 0 0",sep=""))
  20         }
  21         command_line = paste(command_line," /tmp/data_bin",sep="")
  22     }
  23
  24     command_line = paste(command_line," ",args,sep="")
  25     system(command_line)
  26 }
  27
  28 #NOTE: identifiers in first column
  29 getMedoids = function(path=".", xmlResult = "ppamResult.xml",
  30     finalSeries = "ppamFinalSeries.bin")
  31 {
  32     system(paste(path,"/ppam.exe deserialize ",finalSeries," ppamFinalSeries.csv -1",sep=""))
  33     curves = read.table("ppamFinalSeries.csv", sep=",")
  34     library(XML)
  35     ranks = as.integer( xmlToList( xmlParse(xmlResult) )$ranks )
  36     return ( curves[ranks,] ) # == medoids
  37 }
  38
  39 getDistor = function(path=".", xmlResult = "ppamResult.xml",
  40     finalSeries = "ppamFinalSeries.bin")
  41 {
  42     system(paste(path,"/ppam.exe classif ",finalSeries," ",xmlResult,sep=""))
  43 }
  44
  45 serialize = function(path=".", csvSeries, binSeries, byCols=0, nbSeries=0)
  46 {
  47     system(paste(path,"/ppam.exe serialize ",csvSeries," ",binSeries," ",byCols," ",nbSeries,
  48         sep=""))
  49 }
  50
  51 deserialize = function(path=".", binSeries, csvSeries, ranks="-1", return=TRUE)
  52 {
  53     system(paste(path,"/ppam.exe deserialize ",binSeries," ",csvSeries," ",ranks,sep=""))
  54     if (return)
  55         return ( read.table(csvSeries, sep=",") )
  56 }