'update'

[epclust.git] / epclust / R / utils.R

diff --git a/epclust/R/utils.R b/epclust/R/utils.R
new file mode 100644 (file)
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+++ b/epclust/R/utils.R
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+# Check integer arguments with functional conditions
+.toInteger <- function(x, condition)
+{
+       errWarn <- function(ignored)
+               paste("Cannot convert argument' ",substitute(x),"' to integer", sep="")
+       if (!is.integer(x))
+               tryCatch({x = as.integer(x)[1]; if (is.na(x)) stop()},
+                       warning = errWarn, error = errWarn)
+       if (!condition(x))
+       {
+               stop(paste("Argument '",substitute(x),
+                       "' does not verify condition ",body(condition), sep=""))
+       }
+       x
+}
+
+# Check logical arguments
+.toLogical <- function(x)
+{
+       errWarn <- function(ignored)
+               paste("Cannot convert argument' ",substitute(x),"' to logical", sep="")
+       if (!is.logical(x))
+               tryCatch({x = as.logical(x)[1]; if (is.na(x)) stop()},
+                       warning = errWarn, error = errWarn)
+       x
+}
+
+#' curvesToContribs
+#'
+#' Compute the discrete wavelet coefficients for each series, and aggregate them in
+#' energy contribution across scales as described in https://arxiv.org/abs/1101.4744v2
+#'
+#' @param series [big.]matrix of series (in columns), of size L x n
+#' @inheritParams claws
+#'
+#' @return A matrix of size log(L) x n containing contributions in columns
+#'
+#' @export
+curvesToContribs = function(series, wav_filt, contrib_type, coin=FALSE)
+{
+       L = nrow(series)
+       D = ceiling( log2(L) )
+       # Series are interpolated to all have length 2^D
+       nb_sample_points = 2^D
+       apply(series, 2, function(x) {
+               interpolated_curve = spline(1:L, x, n=nb_sample_points)$y
+               W = wavelets::dwt(interpolated_curve, filter=wav_filt, D)@W
+               # Compute the sum of squared discrete wavelet coefficients, for each scale
+               nrj = rev( sapply( W, function(v) ( sqrt( sum(v^2) ) ) ) )
+               if (contrib_type!="absolute")
+                       nrj = nrj / sum(nrj)
+               if (contrib_type=="logit")
+                       nrj = - log(1 - nrj)
+               nrj
+       })
+}
+
+# Helper function to divide indices into balanced sets
+# If max == TRUE, sets sizes cannot exceed nb_per_set
+.splitIndices = function(indices, nb_per_set, max=FALSE)
+{
+       L = length(indices)
+       nb_workers = floor( L / nb_per_set )
+       rem = L %% nb_per_set
+       if (nb_workers == 0 || (nb_workers==1 && rem==0))
+       {
+               # L <= nb_per_set, simple case
+               indices_workers = list(indices)
+       }
+       else
+       {
+               indices_workers = lapply( seq_len(nb_workers), function(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_set
+               while (rem > 0)
+               {
+                       index = rem%%nb_workers + 1
+                       indices_workers[[index]] = c(indices_workers[[index]], indices[L-rem+1])
+                       rem = rem - 1
+               }
+       }
+       indices_workers
+}
+
+#' filterMA
+#'
+#' Filter [time-]series by replacing all values by the moving average of values
+#' centered around current one. Border values are averaged with available data.
+#'
+#' @param M_ A real matrix of size LxD
+#' @param w_ The (odd) number of values to average
+#'
+#' @return The filtered matrix, of same size as the input
+#' @export
+filterMA = function(M_, w_)
+       .Call("filterMA", M_, w_, PACKAGE="epclust")
+
+#' cleanBin
+#'
+#' Remove binary files to re-generate them at next run of \code{claws()}.
+#' Note: run it in the folder where the computations occurred (or no effect).
+#'
+#' @export
+cleanBin <- function()
+{
+       bin_files = list.files(pattern = "*.epclust.bin", all.files=TRUE)
+       for (file in bin_files)
+               unlink(file)
+}