-#' @name clustering
-#' @rdname clustering
-#' @aliases clusteringTask1 computeClusters1 computeClusters2
+#' Two-stage clustering, within one task (see \code{claws()})
#'
-#' @title Two-stage clustering, withing one task (see \code{claws()})
+#' \code{clusteringTask1()} runs one full stage-1 task, which consists in iterated
+#' clustering on nb_curves / ntasks energy contributions, computed through
+#' discrete wavelets coefficients.
+#' \code{clusteringTask2()} runs a full stage-2 task, which consists in WER distances
+#' computations between medoids (indices) output from stage 1, before applying
+#' the second clustering algorithm on the distances matrix.
#'
-#' @description \code{clusteringTask1()} runs one full stage-1 task, which consists in
-#' iterated stage 1 clustering (on nb_curves / ntasks energy contributions, computed
-#' through discrete wavelets coefficients).
-#' \code{clusteringTask2()} runs a full stage-2 task, which consists in synchrones
-#' 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)
-#'
-#' @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
+#' \code{getContribs(indices)} outputs a contributions matrix, in columns
#' @inheritParams claws
+#' @inheritParams computeSynchrones
+#' @inheritParams computeWerDists
+#'
+#' @return The indices of the computed (resp. K1 and K2) medoids.
#'
-#' @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)
+#' @name clustering
+#' @rdname clustering
+#' @aliases clusteringTask1 clusteringTask2
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_clust,
+ ncores_clust=3, verbose=FALSE)
{
if (verbose)
- cat(paste("*** Clustering task 1 on ",length(indices)," lines\n", sep=""))
+ cat(paste("*** Clustering task 1 on ",length(indices)," series [start]\n", sep=""))
+
+ if (length(indices) <= K1)
+ return (indices)
+ parll <- (ncores_clust > 1)
if (parll)
{
- cl = parallel::makeCluster(ncores_clust)
- parallel::clusterExport(cl, varlist=c("getContribs","K1","verbose"), envir=environment())
+ # outfile=="" to see stderr/stdout on terminal
+ cl <-
+ if (verbose)
+ parallel::makeCluster(ncores_clust, outfile = "")
+ else
+ parallel::makeCluster(ncores_clust)
+ 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 <- .splitIndices(indices, nb_items_clust, min_size=K1+1)
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) ]
) )
}
+ if (verbose)
+ {
+ cat(paste("*** Clustering task 1 on ",length(indices)," medoids [iter]\n", sep=""))
+ }
}
if (parll)
parallel::stopCluster(cl)
#' @rdname clustering
#' @export
-clusteringTask2 = function(medoids, K2,
- getRefSeries, nb_ref_curves, nb_series_per_chunk, ncores_clust=1,verbose=FALSE,parll=TRUE)
-{
- if (verbose)
- cat(paste("*** Clustering task 2 on ",nrow(medoids)," lines\n", sep=""))
-
- if (nrow(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)
+clusteringTask2 <- function(indices, getSeries, K2, algoClust2, nb_series_per_chunk,
+ smooth_lvl, nvoice, nbytes, endian, ncores_clust=3, verbose=FALSE)
{
if (verbose)
- cat(paste(" computeClusters1() on ",nrow(contribs)," lines\n", sep=""))
- cluster::pam(contribs, K1, diss=FALSE)$id.med
-}
-
-#' @rdname clustering
-#' @export
-computeClusters2 = function(distances, K2, verbose=FALSE)
-{
- if (verbose)
- cat(paste(" computeClusters2() on ",nrow(distances)," lines\n", sep=""))
- cluster::pam(distances, K2, diss=TRUE)$id.med
-}
-
-#' computeSynchrones
-#'
-#' Compute the synchrones curves (sum of clusters elements) from a matrix of medoids,
-#' using L2 distances.
-#'
-#' @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)
-{
- if (verbose)
- cat(paste("--- Compute synchrones\n", sep=""))
-
- computeSynchronesChunk = function(indices)
- {
- if (parll)
- {
- require("bigmemory", quietly=TRUE)
- requireNamespace("synchronicity", quietly=TRUE)
- require("epclust", quietly=TRUE)
- synchrones <- bigmemory::attach.big.matrix(synchrones_desc)
- counts <- bigmemory::attach.big.matrix(counts_desc)
- medoids <- bigmemory::attach.big.matrix(medoids_desc)
- m <- synchronicity::attach.mutex(m_desc)
- }
-
- ref_series = getRefSeries(indices)
- nb_series = nrow(ref_series)
-
- #get medoids indices for this chunk of series
- mi = computeMedoidsIndices(medoids@address, ref_series)
-
- for (i in seq_len(nb_series))
- {
- if (parll)
- synchronicity::lock(m)
- synchrones[ mi[i], ] = synchrones[ mi[i], ] + ref_series[i,]
- counts[ mi[i] ] = counts[ mi[i] ] + 1 #TODO: remove counts?
- if (parll)
- synchronicity::unlock(m)
- }
- }
-
- K = nrow(medoids) ; L = ncol(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()
- m_desc <- synchronicity::describe(m)
- synchrones_desc = bigmemory::describe(synchrones)
- counts_desc = bigmemory::describe(counts)
- medoids_desc = bigmemory::describe(medoids)
- cl = parallel::makeCluster(ncores_clust)
- parallel::clusterExport(cl, varlist=c("synchrones_desc","counts_desc","counts",
- "verbose","m_desc","medoids_desc","getRefSeries"), envir=environment())
- }
+ cat(paste("*** Clustering task 2 on ",length(indices)," medoids\n", sep=""))
- indices_workers = .spreadIndices(seq_len(nb_ref_curves), nb_series_per_chunk)
- ignored <-
- if (parll)
- parallel::parLapply(cl, indices_workers, computeSynchronesChunk)
- else
- lapply(indices_workers, computeSynchronesChunk)
+ if (length(indices) <= K2)
+ return (indices)
- 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,]
-}
+ # A) Compute the WER distances (Wavelets Extended coefficient of deteRmination)
+ distances <- computeWerDists(indices, getSeries, nb_series_per_chunk,
+ smooth_lvl, nvoice, nbytes, endian, ncores_clust, verbose)
-#' computeWerDists
-#'
-#' Compute the WER distances between the synchrones curves (in rows), 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
-#' @inheritParams claws
-#'
-#' @return A matrix of size K1 x K1
-#'
-#' @export
-computeWerDists = function(synchrones, ncores_clust=1,verbose=FALSE,parll=TRUE)
-{
+ # B) Apply clustering algorithm 2 on the WER distances matrix
if (verbose)
- cat(paste("--- Compute WER dists\n", sep=""))
-
-
-
-
-#TODO: serializer les CWT, les récupérer via getDataInFile
-#--> OK, faut juste stocker comme séries simples de taille delta*ncol (53*17519)
-
-
-
-
- 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
-
- Xwer_dist <- bigmemory::big.matrix(nrow=n, ncol=n, type="double")
-
- # Generate n(n-1)/2 pairs for WER distances computations
-# pairs = list()
-# V = seq_len(n)
-# for (i in 1:n)
-# {
-# V = V[-1]
-# pairs = c(pairs, lapply(V, function(v) c(i,v)))
-# }
- # Generate "smart" pairs for WER distances computations
- pairs = list()
- F = floor(2*n/3)
- for (i in 1:F)
- pairs = c(pairs, lapply((i+1):n, function(v) c(i,v)))
- V = (F+1):n
- for (i in (F+1):(n-1))
- {
- V = V[-1]
- pairs = c(pairs,
-
- # Distance between rows i and j
- computeDistancesIJ = function(pair)
- {
- if (parll)
- {
- require("bigmemory", quietly=TRUE)
- require("epclust", quietly=TRUE)
- synchrones <- bigmemory::attach.big.matrix(synchrones_desc)
- Xwer_dist <- bigmemory::attach.big.matrix(Xwer_dist_desc)
- }
-
- computeCWT = function(index)
- {
- ts <- scale(ts(synchrones[index,]), 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))
- }
-
- i = pair[1] ; j = pair[2]
- if (verbose && j==i+1)
- cat(paste(" Distances (",i,",",j,"), (",i,",",j+1,") ...\n", sep=""))
- cwt_i <- computeCWT(i)
- cwt_j <- computeCWT(j)
-
-#print(system.time( {
- num <- epclustFilter(Mod(cwt_i * Conj(cwt_j)))
- WX <- epclustFilter(Mod(cwt_i * Conj(cwt_i)))
- WY <- epclustFilter(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) * max(1 - wer2, 0.)) #FIXME: wer2 should be < 1
- Xwer_dist[j,i] <- Xwer_dist[i,j]
-#} ) )
- Xwer_dist[i,i] = 0.
- }
-
- if (parll)
- {
- cl = parallel::makeCluster(ncores_clust)
- synchrones_desc <- bigmemory::describe(synchrones)
- Xwer_dist_desc <- bigmemory::describe(Xwer_dist)
-
- parallel::clusterExport(cl, varlist=c("synchrones_desc","Xwer_dist_desc","totnoct",
- "nvoice","w0","s0log","noctave","s0","verbose"), envir=environment())
- }
-
- ignored <-
- if (parll)
- parallel::parLapply(cl, pairs, computeDistancesIJ)
- else
- lapply(pairs, computeDistancesIJ)
-
- if (parll)
- parallel::stopCluster(cl)
-
- Xwer_dist[n,n] = 0.
- distances <- Xwer_dist[,]
- rm(Xwer_dist) ; gc()
- distances #~small matrix K1 x K1
-}
-
-# Helper function to divide indices into balanced sets
-.spreadIndices = function(indices, nb_per_chunk)
-{
- L = length(indices)
- nb_workers = floor( L / nb_per_chunk )
- if (nb_workers == 0)
- {
- # L < nb_series_per_chunk, 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)] )
- # Spread the remaining load among the workers
- rem = L %% nb_per_chunk
- while (rem > 0)
- {
- index = rem%%nb_workers + 1
- indices_workers[[index]] = c(indices_workers[[index]], indices[L-rem+1])
- rem = rem - 1
- }
- }
- indices_workers
+ cat(paste("*** algoClust2() on ",nrow(distances)," items\n", sep=""))
+ indices[ algoClust2(distances,K2) ]
}