Commit | Line | Data |
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73d68777 BA |
1 | ppam_exe = function(path=".", np=parallel::detectCores(), data=NULL, |
2 | args="DontLetMeEmptyPlease!") | |
f1fea222 | 3 | { |
687aed4f | 4 | command_line = paste("mpirun -np ",np," ",path,"/ppam.exe cluster",sep="") |
ebf1280e BA |
5 | |
6 | #if data provided (as data.frame or matrix...): binarize it, and add it as first argument | |
7 | if (!is.null(data)) | |
8 | { | |
f9f51b6a BA |
9 | if (!is.character(data)) |
10 | { | |
73d68777 BA |
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) | |
f9f51b6a BA |
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="") | |
ebf1280e BA |
20 | } |
21 | ||
22 | command_line = paste(command_line," ",args,sep="") | |
f1fea222 BA |
23 | system(command_line) |
24 | } | |
73d68777 BA |
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 | } |