X-Git-Url: https://git.auder.net/?a=blobdiff_plain;f=code%2Fstage1%2Fwrapper.R;h=0a957d8062552459fc7a3a2760242e06627bc6c5;hb=73d68777d709e054cf74e806e23b0bdefda9462a;hp=524fc90cf8628ae4e71564f72795d916a926fc9f;hpb=f9f51b6ab4c7280dd521da675353252d7b078984;p=epclust.git

diff --git a/code/stage1/wrapper.R b/code/stage1/wrapper.R
index 524fc90..0a957d8 100644
--- a/code/stage1/wrapper.R
+++ b/code/stage1/wrapper.R
@@ -1,4 +1,5 @@
-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 cluster",sep="")
 
@@ -7,8 +8,9 @@ ppam_exe = function(path=".", np=parallel::detectCores(), data=NULL, args="DontL
 	{
 		if (!is.character(data))
 		{
-			#assuming matrix or data.frame, WITH row names (identifiers; could be line number...)
-			write.csv(data, "/tmp/data_csv", row.names=TRUE, col.names=FALSE)
+			#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
 		{
@@ -20,3 +22,14 @@ ppam_exe = function(path=".", np=parallel::detectCores(), data=NULL, args="DontL
 	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
+}