X-Git-Url: https://git.auder.net/variants/%24%7Bvname%7D/current/gitweb.css?a=blobdiff_plain;f=code%2Fstage1%2Fwrapper.R;h=0a957d8062552459fc7a3a2760242e06627bc6c5;hb=73d68777d709e054cf74e806e23b0bdefda9462a;hp=9bbb53b035e27b72f76d1dec1b30d6dda3312ba1;hpb=ebf1280e432d51f47238ce8df86750ba3a7d6d1f;p=epclust.git

diff --git a/code/stage1/wrapper.R b/code/stage1/wrapper.R
index 9bbb53b..0a957d8 100644
--- a/code/stage1/wrapper.R
+++ b/code/stage1/wrapper.R
@@ -1,15 +1,35 @@
-ppam_exe = function(path=".", np=parallel::detectCores(), data=NULL, args="DontLetMeEmpty")
+ppam_exe = function(path=".", np=parallel::detectCores(), data=NULL,
+	args="DontLetMeEmptyPlease!")
 {
-	command_line = paste("mpirun -np ",np," ",path,"/ppam.exe",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))
 	{
-		write.csv(data, "/tmp/data_csv")
-		system(paste(path,"/ppam.exe serialize /tmp/data_csv /tmp/data_bin 0 0",sep=""))
-		command_line = paste(command_line," ","/tmp/data_bin",sep="")
+		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
+}