#'
#' @return For \code{clusteringTask1()} and \code{computeClusters1()}, the indices of the
#' computed (K1) medoids. Indices are irrelevant for stage 2 clustering, thus
-#' \code{computeClusters2()} outputs a matrix of medoids
+#' \code{computeClusters2()} outputs a big.matrix of medoids
#' (of size limited by nb_series_per_chunk)
NULL
synchrones = computeSynchrones(medoids,
getRefSeries, nb_ref_curves, nb_series_per_chunk, ncores_clust, verbose, parll)
distances = computeWerDists(synchrones, ncores_clust, verbose, parll)
+ #TODO: if PAM cannot take big.matrix in input, cast it before... (more than OK in RAM)
medoids[ cluster::pam(distances, K2, diss=TRUE)$medoids , ]
}
#' Compute the synchrones curves (sum of clusters elements) from a matrix of medoids,
#' using L2 distances.
#'
-#' @param medoids Matrix of medoids (curves of same legnth as initial series)
+#' @param medoids big.matrix of medoids (curves of same length as initial series)
#' @param getRefSeries Function to retrieve initial series (e.g. in stage 2 after series
#' have been replaced by stage-1 medoids)
#' @param nb_ref_curves How many reference series? (This number is known at this stage)
#' @inheritParams claws
#'
+#' @return A big.matrix of size K1 x L where L = data_length
+#'
#' @export
computeSynchrones = function(medoids, getRefSeries,
nb_ref_curves, nb_series_per_chunk, ncores_clust=1,verbose=FALSE,parll=TRUE)
{
+
+
+
+#TODO: si parll, getMedoids + serialization, pass only getMedoids to nodes
+# --> BOF... chaque node chargera tous les medoids (efficacité) :/ ==> faut que ça tienne en RAM
+#au pire :: C-ifier et charger medoids 1 by 1...
+
+ #MIEUX :: medoids DOIT etre une big.matrix partagée !
+
computeSynchronesChunk = function(indices)
{
if (verbose)
K = nrow(medoids)
# Use bigmemory (shared==TRUE by default) + synchronicity to fill synchrones in //
+ # TODO: if size > RAM (not our case), use file-backed big.matrix
synchrones = bigmemory::big.matrix(nrow=K,ncol=ncol(medoids),type="double",init=0.)
counts = bigmemory::big.matrix(nrow=K,ncol=1,type="double",init=0)
- # Fork (// run) only on Linux & MacOS; on Windows: run sequentially
+ # synchronicity is only for Linux & MacOS; on Windows: run sequentially
parll = (requireNamespace("synchronicity",quietly=TRUE)
&& parll && Sys.info()['sysname'] != "Windows")
if (parll)
m <- synchronicity::boost.mutex()
+ if (parll)
+ {
+ cl = parallel::makeCluster(ncores_clust)
+ parallel::clusterExport(cl,
+ varlist=c("synchrones","counts","verbose","medoids","getRefSeries"),
+ envir=environment())
+ }
+
indices_workers = .spreadIndices(seq_len(nb_ref_curves), nb_series_per_chunk)
ignored <-
if (parll)
- {
- parallel::mclapply(indices_workers, computeSynchronesChunk,
- mc.cores=ncores_clust, mc.allow.recursive=FALSE)
- }
+ parallel::parLapply(indices_workers, computeSynchronesChunk)
else
lapply(indices_workers, computeSynchronesChunk)
- mat_syncs = matrix(nrow=K, ncol=ncol(medoids))
- vec_count = rep(NA, K)
- #TODO: can we avoid this loop?
+ if (parll)
+ parallel::stopCluster(cl)
+
+ #TODO: can we avoid this loop? ( synchrones = sweep(synchrones, 1, counts, '/') )
for (i in seq_len(K))
- {
- mat_syncs[i,] = synchrones[i,]
- vec_count[i] = counts[i,1]
- }
+ synchrones[i,] = synchrones[i,] / counts[i,1]
#NOTE: odds for some clusters to be empty? (when series already come from stage 2)
# ...maybe; but let's hope resulting K1' be still quite bigger than K2
- mat_syncs = sweep(mat_syncs, 1, vec_count, '/')
- mat_syncs[ sapply(seq_len(K), function(i) all(!is.nan(mat_syncs[i,]))) , ]
+ noNA_rows = sapply(seq_len(K), function(i) all(!is.nan(synchrones[i,])))
+ if (all(noNA_rows))
+ return (synchrones)
+ # Else: some clusters are empty, need to slice synchrones
+ synchrones[noNA_rows,]
}
#' computeWerDists
#' Compute the WER distances between the synchrones curves (in rows), which are
#' returned (e.g.) by \code{computeSynchrones()}
#'
-#' @param synchrones A matrix of synchrones, in rows. The series have same length as the
-#' series in the initial dataset
+#' @param synchrones A big.matrix of synchrones, in rows. The series have same length
+#' as the series in the initial dataset
#' @inheritParams claws
#'
+#' @return A big.matrix of size K1 x K1
+#'
#' @export
computeWerDists = function(synchrones, ncores_clust=1,verbose=FALSE,parll=TRUE)
{
+
+
+
+#TODO: re-organize to call computeWerDist(x,y) [C] (in //?) from two indices + big.matrix
+
+
n <- nrow(synchrones)
delta <- ncol(synchrones)
#TODO: automatic tune of all these parameters ? (for other users)
noctave = 13
# 4 here represent 2^5 = 32 half-hours ~ 1 day
#NOTE: default scalevector == 2^(0:(noctave * nvoice) / nvoice) * s0 (?)
- scalevector <- 2^(4:(noctave * nvoice) / nvoice) * 2
+ scalevector <- 2^(4:(noctave * nvoice) / nvoice + 1)
#condition: ( log2(s0*w0/(2*pi)) - 1 ) * nvoice + 1.5 >= 1
s0=2
w0=2*pi
if (verbose)
cat(paste("+++ Compute Rwave::cwt() on serie ",i,"\n", sep=""))
ts <- scale(ts(synchrones[i,]), center=TRUE, scale=scaled)
- totts.cwt = Rwave::cwt(ts,totnoct,nvoice,w0,plot=0)
+ totts.cwt = Rwave::cwt(ts, totnoct, nvoice, w0, plot=FALSE)
ts.cwt = totts.cwt[,s0log:(s0log+noctave*nvoice)]
#Normalization
sqs <- sqrt(2^(0:(noctave*nvoice)/nvoice)*s0)
envir=environment())
}
- # (normalized) observations node with CWT
+ # list of CWT from synchrones
+ # TODO: fit in RAM, OK? If not, 2 options: serialize, compute individual distances
Xcwt4 <-
if (parll)
parallel::parLapply(cl, seq_len(n), computeCWT)
if (verbose)
cat("*** Compute WER distances from CWT\n")
+ #TODO: computeDistances(i,j), et répartir les n(n-1)/2 couples d'indices
+ #là c'est trop déséquilibré
+
computeDistancesLineI = function(i)
{
if (verbose)
num <- filter(Mod(Xcwt4[[i]] * Conj(Xcwt4[[j]])), fcoefs, circular=TRUE)
WX <- filter(Mod(Xcwt4[[i]] * Conj(Xcwt4[[i]])), fcoefs, circular=TRUE)
WY <- filter(Mod(Xcwt4[[j]] * Conj(Xcwt4[[j]])), fcoefs, circular=TRUE)
- wer2 <- sum(colSums(num)^2) / sum( sum(colSums(WX) * colSums(WY)) )
+ wer2 <- sum(colSums(num)^2) / sum( sum(colSums(WX) * colSums(WY)) )
if (parll)
synchronicity::lock(m)
Xwer_dist[i,j] <- sqrt(delta * ncol(Xcwt4[[1]]) * (1 - wer2))
else
lapply(seq_len(n-1), computeDistancesLineI)
Xwer_dist[n,n] = 0.
-
- mat_dists = matrix(nrow=n, ncol=n)
- #TODO: avoid this loop?
- for (i in 1:n)
- mat_dists[i,] = Xwer_dist[i,]
- mat_dists
+ Xwer_dist
}
# Helper function to divide indices into balanced sets
--- /dev/null
+#include <stdlib.h>
+#include <math.h>
+#include <stdbool.h>
+
+#ifndef M_PI
+#define M_PI 3.14159265358979323846
+#endif
+
+// n: number of synchrones, m: length of a synchrone
+float computeWerDist(float* s1, float* s2, int n, int m)
+{
+ //TODO: automatic tune of all these parameters ? (for other users)
+ int nvoice = 4;
+ //noctave 2^13 = 8192 half hours ~ 180 days ; ~log2(ncol(synchrones))
+ int noctave = 13
+ // 4 here represent 2^5 = 32 half-hours ~ 1 day
+ //NOTE: default scalevector == 2^(0:(noctave * nvoice) / nvoice) * s0 (?)
+ //R: scalevector <- 2^(4:(noctave * nvoice) / nvoice + 1)
+ int* scalevector = (int*)malloc( (noctave*nvoice-4 + 1) * sizeof(int))
+ for (int i=4; i<=noctave*nvoice; i++)
+ scalevector[i-4] = pow(2., (float)i/nvoice + 1.);
+ //condition: ( log2(s0*w0/(2*pi)) - 1 ) * nvoice + 1.5 >= 1
+ int s0 = 2;
+ double w0 = 2*M_PI;
+ bool scaled = false;
+ int s0log = as.integer( (log2( s0*w0/(2*pi) ) - 1) * nvoice + 1.5 )
+ int totnoct = noctave + as.integer(s0log/nvoice) + 1
+
+
+
+
+
+///TODO: continue
+
+
+
+ computeCWT = function(i)
+ {
+ if (verbose)
+ cat(paste("+++ Compute Rwave::cwt() on serie ",i,"\n", sep=""))
+ ts <- scale(ts(synchrones[i,]), center=TRUE, scale=scaled)
+ totts.cwt = Rwave::cwt(ts,totnoct,nvoice,w0,plot=0)
+ ts.cwt = totts.cwt[,s0log:(s0log+noctave*nvoice)]
+ #Normalization
+ sqs <- sqrt(2^(0:(noctave*nvoice)/nvoice)*s0)
+ sqres <- sweep(ts.cwt,2,sqs,'*')
+ sqres / max(Mod(sqres))
+ }
+
+ if (parll)
+ {
+ cl = parallel::makeCluster(ncores_clust)
+ parallel::clusterExport(cl,
+ varlist=c("synchrones","totnoct","nvoice","w0","s0log","noctave","s0","verbose"),
+ envir=environment())
+ }
+
+ # (normalized) observations node with CWT
+ Xcwt4 <-
+ if (parll)
+ parallel::parLapply(cl, seq_len(n), computeCWT)
+ else
+ lapply(seq_len(n), computeCWT)
+
+ if (parll)
+ parallel::stopCluster(cl)
+
+ Xwer_dist <- bigmemory::big.matrix(nrow=n, ncol=n, type="double")
+ fcoefs = rep(1/3, 3) #moving average on 3 values (TODO: very slow! correct?!)
+ if (verbose)
+ cat("*** Compute WER distances from CWT\n")
+
+ #TODO: computeDistances(i,j), et répartir les n(n-1)/2 couples d'indices
+ #là c'est trop déséquilibré
+
+ computeDistancesLineI = function(i)
+ {
+ if (verbose)
+ cat(paste(" Line ",i,"\n", sep=""))
+ for (j in (i+1):n)
+ {
+ #TODO: 'circular=TRUE' is wrong, should just take values on the sides; to rewrite in C
+ num <- filter(Mod(Xcwt4[[i]] * Conj(Xcwt4[[j]])), fcoefs, circular=TRUE)
+ WX <- filter(Mod(Xcwt4[[i]] * Conj(Xcwt4[[i]])), fcoefs, circular=TRUE)
+ WY <- filter(Mod(Xcwt4[[j]] * Conj(Xcwt4[[j]])), fcoefs, circular=TRUE)
+ wer2 <- sum(colSums(num)^2) / sum( sum(colSums(WX) * colSums(WY)) )
+ if (parll)
+ synchronicity::lock(m)
+ Xwer_dist[i,j] <- sqrt(delta * ncol(Xcwt4[[1]]) * (1 - wer2))
+ Xwer_dist[j,i] <- Xwer_dist[i,j]
+ if (parll)
+ synchronicity::unlock(m)
+ }
+ Xwer_dist[i,i] = 0.
+ }
+
+ parll = (requireNamespace("synchronicity",quietly=TRUE)
+ && parll && Sys.info()['sysname'] != "Windows")
+ if (parll)
+ m <- synchronicity::boost.mutex()
+
+ ignored <-
+ if (parll)
+ {
+ parallel::mclapply(seq_len(n-1), computeDistancesLineI,
+ mc.cores=ncores_clust, mc.allow.recursive=FALSE)
+ }
+ else
+ lapply(seq_len(n-1), computeDistancesLineI)
+ Xwer_dist[n,n] = 0.
+
+ mat_dists = matrix(nrow=n, ncol=n)
+ #TODO: avoid this loop?
+ for (i in 1:n)
+ mat_dists[i,] = Xwer_dist[i,]
+ mat_dists
+
projects / epclust.git / commitdiff