{
ref_series = getRefSeries(indices)
nb_series = nrow(ref_series)
- #get medoids indices for this chunk of series
- #TODO: debug this (address is OK but values are garbage: why?)
-# mi = .Call("computeMedoidsIndices", medoids@address, ref_series, PACKAGE="epclust")
+ if (parll)
+ {
+ require("bigmemory", quietly=TRUE)
+ require("synchronicity", quietly=TRUE)
+ require("epclust", quietly=TRUE)
+ synchrones <- bigmemory::attach.big.matrix(synchrones_desc)
+ medoids <- bigmemory::attach.big.matrix(medoids_desc)
+ m <- synchronicity::attach.mutex(m_desc)
+ }
- #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)
+# #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()
for (i in seq_len(nb_series))
{
if (parll)
synchronicity::lock(m)
synchrones[mi[i],] = synchrones[mi[i],] + ref_series[i,]
+#TODO: remove counts
counts[mi[i],1] = counts[mi[i],1] + 1
if (parll)
synchronicity::unlock(m)
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)
+ medoids_desc = bigmemory::describe(medoids)
- if (parll)
- {
cl = parallel::makeCluster(ncores_clust)
parallel::clusterExport(cl,
- varlist=c("synchrones","counts","verbose","medoids","getRefSeries"),
+ varlist=c("synchrones_desc","counts","verbose","m_desc","medoids_desc","getRefSeries"),
envir=environment())
}
indices_workers = .spreadIndices(seq_len(nb_ref_curves), nb_series_per_chunk)
-#browser()
ignored <-
if (parll)
parallel::parLapply(cl, indices_workers, computeSynchronesChunk)
pairs = c(pairs, lapply(V, function(v) c(i,v)))
}
- computeCWT = function(i)
- {
- 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))
- }
-
# 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))
+ }
+#browser()
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)
- 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")
+print(system.time( { 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) * (1 - wer2))
+ 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)
- parallel::clusterExport(cl,
- varlist=c("synchrones","totnoct","nvoice","w0","s0log","noctave","s0","verbose"),
- envir=environment())
- }
+ 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())
+ }
+browser()
ignored <-
if (parll)
parallel::parLapply(cl, pairs, computeDistancesIJ)
if (parll)
parallel::stopCluster(cl)
-
+#browser()
Xwer_dist[n,n] = 0.
distances <- Xwer_dist[,]
rm(Xwer_dist) ; gc()
projects / epclust.git / blobdiff