+ 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")
+
+ # 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)))
+ }
+
+ cwt_file = ".cwt.bin"
+ # Compute the synchrones[,index] CWT, and store it in the binary file above
+ computeSaveCWT = function(index)
+ {
+ 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)
+ }
+
+ 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 && !parll)
+ cat(paste(" Distances (",i,",",j,"), (",i,",",j+1,") ...\n", sep=""))
+
+ # 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(L * ncol(cwt_i) * (1 - wer2))
+ Xwer_dist[j,i] <- Xwer_dist[i,j]
+ Xwer_dist[i,i] <- 0.
+ }
+
+ if (verbose)
+ cat(paste("--- Compute WER distances\n", sep=""))
+
+ ignored <-
+ if (parll)
+ parallel::parLapply(cl, pairs, computeDistanceIJ)
+ else
+ lapply(pairs, computeDistanceIJ)
+
+ if (parll)
+ parallel::stopCluster(cl)
+
+ unlink(cwt_file)
+
+ Xwer_dist[n,n] = 0.
+ Xwer_dist[,] #~small matrix K1 x K1