| 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 | } |