X-Git-Url: https://git.auder.net/css/rpsls.css?a=blobdiff_plain;f=code%2Fstage1%2Fwrapper.R;h=0a957d8062552459fc7a3a2760242e06627bc6c5;hb=38aef1cbef037257bf03dd1e65fbb682a32e3f2c;hp=2549f1fa3d60fb09cdf68d05a1d011aa1e4e79fb;hpb=f1fea2229d365a222b5aff0cb1b4d346c4437e8b;p=epclust.git

diff --git a/code/stage1/wrapper.R b/code/stage1/wrapper.R
index 2549f1f..0a957d8 100644
--- a/code/stage1/wrapper.R
+++ b/code/stage1/wrapper.R
@@ -1,9 +1,35 @@
-ppam_exe = function(pathToExe, nbProcess, ...)
+ppam_exe = function(path=".", np=parallel::detectCores(), data=NULL,
+	args="DontLetMeEmptyPlease!")
 {
-	command_line = paste("mpirun -np ",nbProcess," ",pathToExe,"/ppam.exe",sep="")
-	args = list(...)
-	for (i in 1:length(args))
-		command_line = paste(command_line, args[[i]])
-	print(paste("EXECUTE: '", command_line,"'",sep=""))
+	command_line = paste("mpirun -np ",np," ",path,"/ppam.exe cluster",sep="")
+
+	#if data provided (as data.frame or matrix...): binarize it, and add it as first argument
+	if (!is.null(data))
+	{
+		if (!is.character(data))
+		{
+			#assuming matrix or data.frame, WITH row names
+			#( identifiers; could be line number... e.g. data <- cbind(1:nrow(data),data) )
+			write.table(data, "/tmp/data_csv", sep=",", row.names=FALSE, col.names=FALSE)
+			system(paste(path,"/ppam.exe serialize /tmp/data_csv /tmp/data_bin 0 0",sep=""))
+		} else
+		{
+			system(paste(path,"/ppam.exe serialize ",data," /tmp/data_bin 0 0",sep=""))
+		}
+		command_line = paste(command_line," /tmp/data_bin",sep="")
+	}
+
+	command_line = paste(command_line," ",args,sep="")
 	system(command_line)
 }
+
+#NOTE: identifiers in first column
+getMedoids = function(path=".", xmlResult = "ppamResult.xml",
+	finalSeries = "ppamFinalSeries.bin")
+{
+	system(paste(path,"/ppam.exe deserialize ",finalSeries," ppamFinalSeries.csv -1",sep=""))
+	curves = read.table("ppamFinalSeries.csv", sep=",")
+	library(XML)
+	ranks = as.integer( xmlToList( xmlParse(xmlResult) )$ranks )
+	return ( curves[ranks,] ) # == medoids
+}