| 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 | } |