Commit | Line | Data |
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73d68777 | 1 | ppam_exe = function(path=".", np=parallel::detectCores(), data=NULL, |
14cb6cf8 | 2 | nbSeriesPerChunk, nbClusters, randomize=1, p_dissims=2) |
f1fea222 | 3 | { |
14cb6cf8 BA |
4 | args = paste(nbSeriesPerChunk," ",nbClusters," ",randomize," ",p_dissims,sep="") |
5 | ||
687aed4f | 6 | command_line = paste("mpirun -np ",np," ",path,"/ppam.exe cluster",sep="") |
ebf1280e BA |
7 | |
8 | #if data provided (as data.frame or matrix...): binarize it, and add it as first argument | |
9 | if (!is.null(data)) | |
10 | { | |
f9f51b6a BA |
11 | if (!is.character(data)) |
12 | { | |
73d68777 BA |
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) | |
f9f51b6a BA |
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="") | |
ebf1280e BA |
22 | } |
23 | ||
24 | command_line = paste(command_line," ",args,sep="") | |
f1fea222 BA |
25 | system(command_line) |
26 | } | |
73d68777 BA |
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 | } | |
7709d507 | 38 | |
7709d507 BA |
39 | getDistor = function(path=".", xmlResult = "ppamResult.xml", |
40 | finalSeries = "ppamFinalSeries.bin") | |
41 | { | |
42 | system(paste(path,"/ppam.exe classif ",finalSeries," ",xmlResult,sep="")) | |
43 | } | |
5edda192 BA |
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 | ||
14cb6cf8 | 51 | deserialize = function(path=".", binSeries, csvSeries, ranks="-1", return=TRUE) |
5edda192 BA |
52 | { |
53 | system(paste(path,"/ppam.exe deserialize ",binSeries," ",csvSeries," ",ranks,sep="")) | |
14cb6cf8 BA |
54 | if (return) |
55 | return ( read.table(csvSeries, sep=",") ) | |
5edda192 | 56 | } |