#' @name clustering
#' @rdname clustering
-#' @aliases clusteringTask1 computeClusters1 computeClusters2
+#' @aliases clusteringTask1 clusteringTask2 computeClusters1 computeClusters2
#'
#' @title Two-stage clustering, withing one task (see \code{claws()})
#'
#' and then WER distances computations, before applying the clustering algorithm.
#' \code{computeClusters1()} and \code{computeClusters2()} correspond to the atomic
#' clustering procedures respectively for stage 1 and 2. The former applies the
-#' clustering algorithm (PAM) on a contributions matrix, while the latter clusters
-#' a chunk of series inside one task (~max nb_series_per_chunk)
+#' first clustering algorithm on a contributions matrix, while the latter clusters
+#' a set of series inside one task (~nb_items_clust1)
#'
#' @param indices Range of series indices to cluster in parallel (initial data)
#' @param getContribs Function to retrieve contributions from initial series indices:
#' \code{getContribs(indices)} outpus a contributions matrix
-#' @param contribs matrix of contributions (e.g. output of \code{curvesToContribs()})
-#' @param distances matrix of K1 x K1 (WER) distances between synchrones
#' @inheritParams computeSynchrones
#' @inheritParams claws
#'
-#' @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 big.matrix of medoids
-#' (of size limited by nb_series_per_chunk)
+#' @return For \code{clusteringTask1()}, the indices of the computed (K1) medoids.
+#' Indices are irrelevant for stage 2 clustering, thus \code{clusteringTask2()}
+#' outputs a big.matrix of medoids (of size LxK2, K2 = final number of clusters)
NULL
#' @rdname clustering
#' @export
-clusteringTask1 = function(
- indices, getContribs, K1, nb_series_per_chunk, ncores_clust=1, verbose=FALSE, parll=TRUE)
+clusteringTask1 = function(indices, getContribs, K1, algoClust1, nb_items_clust1,
+ ncores_clust=1, verbose=FALSE, parll=TRUE)
{
- if (verbose)
- cat(paste("*** Clustering task 1 on ",length(indices)," lines\n", sep=""))
-
if (parll)
{
- cl = parallel::makeCluster(ncores_clust)
- parallel::clusterExport(cl, varlist=c("getContribs","K1","verbose"), envir=environment())
+ cl = parallel::makeCluster(ncores_clust, outfile = "")
+ parallel::clusterExport(cl, c("getContribs","K1","verbose"), envir=environment())
}
+ # Iterate clustering algorithm 1 until K1 medoids are found
while (length(indices) > K1)
{
- indices_workers = .spreadIndices(indices, nb_series_per_chunk)
+ # Balance tasks by splitting the indices set - as evenly as possible
+ indices_workers = .spreadIndices(indices, nb_items_clust1)
+ if (verbose)
+ cat(paste("*** [iterated] Clustering task 1 on ",length(indices)," series\n", sep=""))
indices <-
if (parll)
{
unlist( parallel::parLapply(cl, indices_workers, function(inds) {
require("epclust", quietly=TRUE)
- inds[ computeClusters1(getContribs(inds), K1, verbose) ]
+ inds[ algoClust1(getContribs(inds), K1) ]
}) )
}
else
{
unlist( lapply(indices_workers, function(inds)
- inds[ computeClusters1(getContribs(inds), K1, verbose) ]
+ inds[ algoClust1(getContribs(inds), K1) ]
) )
}
}
#' @rdname clustering
#' @export
-clusteringTask2 = function(medoids, K2,
- getRefSeries, nb_ref_curves, nb_series_per_chunk, ncores_clust=1,verbose=FALSE,parll=TRUE)
+clusteringTask2 = function(medoids, K2, algoClust2, getRefSeries, nb_ref_curves,
+ nb_series_per_chunk, nvoice, nbytes,endian,ncores_clust=1,verbose=FALSE,parll=TRUE)
{
if (verbose)
- cat(paste("*** Clustering task 2 on ",nrow(medoids)," lines\n", sep=""))
+ cat(paste("*** Clustering task 2 on ",ncol(medoids)," synchrones\n", sep=""))
- if (nrow(medoids) <= K2)
+ if (ncol(medoids) <= K2)
return (medoids)
- synchrones = computeSynchrones(medoids,
- getRefSeries, nb_ref_curves, nb_series_per_chunk, ncores_clust, verbose, parll)
- distances = computeWerDists(synchrones, ncores_clust, verbose, parll)
- medoids[ computeClusters2(distances,K2,verbose), ]
-}
-#' @rdname clustering
-#' @export
-computeClusters1 = function(contribs, K1, verbose=FALSE)
-{
- if (verbose)
- cat(paste(" computeClusters1() on ",nrow(contribs)," lines\n", sep=""))
- cluster::pam(contribs, K1, diss=FALSE)$id.med
-}
+ # A) Obtain synchrones, that is to say the cumulated power consumptions
+ # for each of the K1 initial groups
+ synchrones = computeSynchrones(medoids, getRefSeries, nb_ref_curves,
+ nb_series_per_chunk, ncores_clust, verbose, parll)
-#' @rdname clustering
-#' @export
-computeClusters2 = function(distances, K2, verbose=FALSE)
-{
+ # B) Compute the WER distances (Wavelets Extended coefficient of deteRmination)
+ distances = computeWerDists(
+ synchrones, nvoice, nbytes, endian, ncores_clust, verbose, parll)
+
+ # C) Apply clustering algorithm 2 on the WER distances matrix
if (verbose)
- cat(paste(" computeClusters2() on ",nrow(distances)," lines\n", sep=""))
- cluster::pam(distances, K2, diss=TRUE)$id.med
+ cat(paste("*** algoClust2() on ",nrow(distances)," items\n", sep=""))
+ medoids[ ,algoClust2(distances,K2) ]
}
#' computeSynchrones
#'
#' Compute the synchrones curves (sum of clusters elements) from a matrix of medoids,
-#' using L2 distances.
+#' using euclidian distance.
#'
#' @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
#' @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
+#' @return A big.matrix of size L x K1 where L = length of a serie
#'
#' @export
-computeSynchrones = function(medoids, getRefSeries,
- nb_ref_curves, nb_series_per_chunk, ncores_clust=1,verbose=FALSE,parll=TRUE)
+computeSynchrones = function(medoids, getRefSeries, nb_ref_curves,
+ nb_series_per_chunk, ncores_clust=1,verbose=FALSE,parll=TRUE)
{
- if (verbose)
- cat(paste("--- Compute synchrones\n", sep=""))
-
+ # Synchrones computation is embarassingly parallel: compute it by chunks of series
computeSynchronesChunk = function(indices)
{
- ref_series = getRefSeries(indices)
- nb_series = nrow(ref_series)
- #get medoids indices for this chunk of series
+ if (parll)
+ {
+ require("bigmemory", quietly=TRUE)
+ requireNamespace("synchronicity", quietly=TRUE)
+ require("epclust", quietly=TRUE)
+ # The big.matrix objects need to be attached to be usable on the workers
+ synchrones <- bigmemory::attach.big.matrix(synchrones_desc)
+ medoids <- bigmemory::attach.big.matrix(medoids_desc)
+ m <- synchronicity::attach.mutex(m_desc)
+ }
- #TODO: debug this (address is OK but values are garbage: why?)
-# mi = .Call("computeMedoidsIndices", medoids@address, ref_series, PACKAGE="epclust")
+ # Obtain a chunk of reference series
+ ref_series = getRefSeries(indices)
+ nb_series = ncol(ref_series)
- #R-equivalent, requiring a matrix (thus potentially breaking "fit-in-memory" hope)
- mat_meds = medoids[,]
- mi = rep(NA,nb_series)
- for (i in 1:nb_series)
- mi[i] <- which.min( rowSums( sweep(mat_meds, 2, ref_series[i,], '-')^2 ) )
- rm(mat_meds); gc()
+ # Get medoids indices for this chunk of series
+ mi = computeMedoidsIndices(medoids@address, ref_series)
+ # Update synchrones using mi above
for (i in seq_len(nb_series))
{
if (parll)
- synchronicity::lock(m)
- synchrones[mi[i],] = synchrones[mi[i],] + ref_series[i,]
- counts[mi[i],1] = counts[mi[i],1] + 1
+ synchronicity::lock(m) #locking required because several writes at the same time
+ synchrones[, mi[i] ] = synchrones[, mi[i] ] + ref_series[,i]
if (parll)
synchronicity::unlock(m)
}
+ NULL
}
- K = nrow(medoids) ; L = ncol(medoids)
+ K = ncol(medoids) ; L = 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=L, type="double", init=0.)
- counts = bigmemory::big.matrix(nrow=K, ncol=1, type="double", init=0)
- # 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()
-
+ synchrones = bigmemory::big.matrix(nrow=L, ncol=K, type="double", init=0.)
+ # NOTE: synchronicity is only for Linux & MacOS; on Windows: run sequentially
+ parll = (parll && requireNamespace("synchronicity",quietly=TRUE)
+ && Sys.info()['sysname'] != "Windows")
if (parll)
{
+ m <- synchronicity::boost.mutex() #for lock/unlock, see computeSynchronesChunk
+ # mutex and big.matrix objects cannot be passed directly:
+ # they will be accessed from their description
+ m_desc <- synchronicity::describe(m)
+ synchrones_desc = bigmemory::describe(synchrones)
+ medoids_desc = bigmemory::describe(medoids)
cl = parallel::makeCluster(ncores_clust)
- parallel::clusterExport(cl,
- varlist=c("synchrones","counts","verbose","medoids","getRefSeries"),
- envir=environment())
+ parallel::clusterExport(cl, envir=environment(),
+ varlist=c("synchrones_desc","m_desc","medoids_desc","getRefSeries"))
}
- indices_workers = .spreadIndices(seq_len(nb_ref_curves), nb_series_per_chunk)
-#browser()
+ if (verbose)
+ cat(paste("--- Compute ",K," synchrones with ",nb_ref_curves," series\n", sep=""))
+
+ # Balance tasks by splitting the indices set - maybe not so evenly, but
+ # max==TRUE in next call ensures that no set has more than nb_series_per_chunk items.
+ indices_workers = .spreadIndices(seq_len(nb_ref_curves), nb_series_per_chunk, max=TRUE)
ignored <-
if (parll)
parallel::parLapply(cl, indices_workers, computeSynchronesChunk)
if (parll)
parallel::stopCluster(cl)
- #TODO: can we avoid this loop? ( synchrones = sweep(synchrones, 1, counts, '/') )
- for (i in seq_len(K))
- 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
- 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,]
+ return (synchrones)
}
#' computeWerDists
#'
-#' Compute the WER distances between the synchrones curves (in rows), which are
+#' Compute the WER distances between the synchrones curves (in columns), which are
#' returned (e.g.) by \code{computeSynchrones()}
#'
-#' @param synchrones A big.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 columns. The series have same
+#' length as the series in the initial dataset
#' @inheritParams claws
#'
-#' @return A matrix of size K1 x K1
+#' @return A distances matrix of size K1 x K1
#'
#' @export
-computeWerDists = function(synchrones, ncores_clust=1,verbose=FALSE,parll=TRUE)
+computeWerDists = function(synchrones, nvoice, nbytes,endian,ncores_clust=1,
+ verbose=FALSE,parll=TRUE)
{
- if (verbose)
- cat(paste("--- Compute WER dists\n", sep=""))
-
- n <- nrow(synchrones)
- delta <- ncol(synchrones)
- #TODO: automatic tune of all these parameters ? (for other users)
- nvoice <- 4
- # noctave = 2^13 = 8192 half hours ~ 180 days ; ~log2(ncol(synchrones))
- 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 + 1)
- #condition: ( log2(s0*w0/(2*pi)) - 1 ) * nvoice + 1.5 >= 1
- s0=2
- w0=2*pi
- scaled=FALSE
- s0log = as.integer( (log2( s0*w0/(2*pi) ) - 1) * nvoice + 1.5 )
- totnoct = noctave + as.integer(s0log/nvoice) + 1
+ n <- ncol(synchrones)
+ L <- nrow(synchrones)
+ noctave = ceiling(log2(L)) #min power of 2 to cover serie range
+ # Initialize result as a square big.matrix of size 'number of synchrones'
Xwer_dist <- bigmemory::big.matrix(nrow=n, ncol=n, type="double")
- fcoefs = rep(1/3, 3) #moving average on 3 values
# Generate n(n-1)/2 pairs for WER distances computations
pairs = list()
pairs = c(pairs, lapply(V, function(v) c(i,v)))
}
- computeCWT = function(i)
+ cwt_file = ".cwt.bin"
+ # Compute the synchrones[,index] CWT, and store it in the binary file above
+ computeSaveCWT = function(index)
{
- ts <- scale(ts(synchrones[i,]), center=TRUE, scale=scaled)
- 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)
- sqres <- sweep(ts.cwt,2,sqs,'*')
- sqres / max(Mod(sqres))
+ if (parll && !exists(synchrones)) #avoid going here after first call on a worker
+ {
+ require("bigmemory", quietly=TRUE)
+ require("Rwave", quietly=TRUE)
+ require("epclust", quietly=TRUE)
+ synchrones <- bigmemory::attach.big.matrix(synchrones_desc)
+ }
+ ts <- scale(ts(synchrones[,index]), center=TRUE, scale=FALSE)
+ ts_cwt = Rwave::cwt(ts, noctave, nvoice, w0=2*pi, twoD=TRUE, plot=FALSE)
+
+ # Serialization
+ binarize(as.matrix(c(as.double(Re(ts_cwt)),as.double(Im(ts_cwt)))), cwt_file, 1,
+ ",", nbytes, endian)
}
- # Distance between rows i and j
- computeDistancesIJ = function(pair)
+ if (parll)
{
+ cl = parallel::makeCluster(ncores_clust)
+ synchrones_desc <- bigmemory::describe(synchrones)
+ Xwer_dist_desc <- bigmemory::describe(Xwer_dist)
+ parallel::clusterExport(cl, varlist=c("parll","synchrones_desc","Xwer_dist_desc",
+ "noctave","nvoice","verbose","getCWT"), envir=environment())
+ }
+
+ if (verbose)
+ cat(paste("--- Precompute and serialize synchrones CWT\n", sep=""))
+
+ ignored <-
+ if (parll)
+ parallel::parLapply(cl, 1:n, computeSaveCWT)
+ else
+ lapply(1:n, computeSaveCWT)
+
+ # Function to retrieve a synchrone CWT from (binary) file
+ getSynchroneCWT = function(index, L)
+ {
+ flat_cwt <- getDataInFile(index, cwt_file, nbytes, endian)
+ cwt_length = length(flat_cwt) / 2
+ re_part = as.matrix(flat_cwt[1:cwt_length], nrow=L)
+ im_part = as.matrix(flat_cwt[(cwt_length+1):(2*cwt_length)], nrow=L)
+ re_part + 1i * im_part
+ }
+
+ # Compute distance between columns i and j in synchrones
+ computeDistanceIJ = function(pair)
+ {
+ if (parll)
+ {
+ # parallel workers start with an empty environment
+ require("bigmemory", quietly=TRUE)
+ require("epclust", quietly=TRUE)
+ synchrones <- bigmemory::attach.big.matrix(synchrones_desc)
+ Xwer_dist <- bigmemory::attach.big.matrix(Xwer_dist_desc)
+ }
+
i = pair[1] ; j = pair[2]
- if (verbose && j==i+1)
+ if (verbose && j==i+1 && !parll)
cat(paste(" Distances (",i,",",j,"), (",i,",",j+1,") ...\n", sep=""))
- cwt_i = computeCWT(i)
- cwt_j = computeCWT(j)
- num <- .Call("filter", Mod(cwt_i * Conj(cwt_j)), PACKAGE="epclust")
- WX <- .Call("filter", Mod(cwt_i * Conj(cwt_i)), PACKAGE="epclust")
- WY <- .Call("filter", Mod(cwt_j * Conj(cwt_j)), PACKAGE="epclust")
+
+ # Compute CWT of columns i and j in synchrones
+ L = nrow(synchrones)
+ cwt_i <- getSynchroneCWT(i, L)
+ cwt_j <- getSynchroneCWT(j, L)
+
+ # Compute the ratio of integrals formula 5.6 for WER^2
+ # in https://arxiv.org/abs/1101.4744v2 ยง5.3
+ num <- filterMA(Mod(cwt_i * Conj(cwt_j)))
+ WX <- filterMA(Mod(cwt_i * Conj(cwt_i)))
+ WY <- filterMA(Mod(cwt_j * Conj(cwt_j)))
wer2 <- sum(colSums(num)^2) / sum(colSums(WX) * colSums(WY))
- Xwer_dist[i,j] <- sqrt(delta * ncol(cwt_i) * (1 - wer2))
+
+ Xwer_dist[i,j] <- sqrt(L * ncol(cwt_i) * (1 - wer2))
Xwer_dist[j,i] <- Xwer_dist[i,j]
- Xwer_dist[i,i] = 0.
+ Xwer_dist[i,i] <- 0.
}
- if (parll)
- {
- cl = parallel::makeCluster(ncores_clust)
- parallel::clusterExport(cl,
- varlist=c("synchrones","totnoct","nvoice","w0","s0log","noctave","s0","verbose"),
- envir=environment())
- }
+ if (verbose)
+ cat(paste("--- Compute WER distances\n", sep=""))
ignored <-
if (parll)
- parallel::parLapply(cl, pairs, computeDistancesIJ)
+ parallel::parLapply(cl, pairs, computeDistanceIJ)
else
- lapply(pairs, computeDistancesIJ)
+ lapply(pairs, computeDistanceIJ)
if (parll)
parallel::stopCluster(cl)
+ unlink(cwt_file)
+
Xwer_dist[n,n] = 0.
- distances <- Xwer_dist[,]
- rm(Xwer_dist) ; gc()
- distances #~small matrix K1 x K1
+ Xwer_dist[,] #~small matrix K1 x K1
}
# Helper function to divide indices into balanced sets
-.spreadIndices = function(indices, nb_per_chunk)
+# If max == TRUE, sets sizes cannot exceed nb_per_set
+.spreadIndices = function(indices, nb_per_set, max=FALSE)
{
L = length(indices)
- nb_workers = floor( L / nb_per_chunk )
- if (nb_workers == 0)
+ nb_workers = floor( L / nb_per_set )
+ rem = L %% nb_per_set
+ if (nb_workers == 0 || (nb_workers==1 && rem==0))
{
- # L < nb_series_per_chunk, simple case
+ # L <= nb_per_set, simple case
indices_workers = list(indices)
}
else
{
indices_workers = lapply( seq_len(nb_workers), function(i)
- indices[(nb_per_chunk*(i-1)+1):(nb_per_chunk*i)] )
+ indices[(nb_per_set*(i-1)+1):(nb_per_set*i)] )
+
+ if (max)
+ {
+ # Sets are not so well balanced, but size is supposed to be critical
+ return ( c( indices_workers, if (rem>0) list((L-rem+1):L) else NULL ) )
+ }
+
# Spread the remaining load among the workers
- rem = L %% nb_per_chunk
+ rem = L %% nb_per_set
while (rem > 0)
{
index = rem%%nb_workers + 1