complete first draft of package

[epclust.git] / epclust / R / main.R

diff --git a/epclust/R/main.R b/epclust/R/main.R
index ac4ea8d..27fbb74 100644 (file)
--- a/epclust/R/main.R
+++ b/epclust/R/main.R
@@ -34,12 +34,13 @@
 #'     "LIMIT ", n, " ORDER BY date", sep=""))
 #'   return (df)
 #' }
+#' #####TODO: if DB, array rank --> ID at first retrieval, when computing coeffs; so:: NO use of IDs !
 #'   #TODO: 3 examples, data.frame / binary file / DB sqLite
 #'   + sampleCurves : wavBootstrap de package wmtsa
 #' cl = epclust(getData, K1=200, K2=15, ntasks=1000, nb_series_per_chunk=5000, WER="mix")
 #' @export
 epclust = function(series,K1,K2,ntasks=1,nb_series_per_chunk=50*K1,min_series_per_chunk=5*K1,
-       wf="haar",WER="end",ncores_tasks=1,ncores_clust=4,random=TRUE,...)
+       wf="haar",WER="end",ncores_tasks=1,ncores_clust=4,random=TRUE,ftype="float",...)
 {
        # Check/transform arguments
        bin_dir = "epclust.bin/"
@@ -50,7 +51,7 @@ epclust = function(series,K1,K2,ntasks=1,nb_series_per_chunk=50*K1,min_series_pe
                unlink(series_file)
        }
        if (is.matrix(series))
-               serialize(series, series_file)
+               serialize(series, series_file, ftype, nb_series_per_chunk)
        else if (!is.function(series))
        {
                tryCatch(
@@ -62,7 +63,7 @@ epclust = function(series,K1,K2,ntasks=1,nb_series_per_chunk=50*K1,min_series_pe
                                        open(series)
                                        series_con = series
                                }
-                               serialize(series_con, series_file)
+                               serialize(series_con, series_file, ftype, nb_series_per_chunk)
                                close(series_con)
                        },
                        error=function(e) "series should be a data.frame, a function or a valid connection"
@@ -93,12 +94,11 @@ epclust = function(series,K1,K2,ntasks=1,nb_series_per_chunk=50*K1,min_series_pe
                if (is.null(series))
                        break
                coeffs_chunk = curvesToCoeffs(series, wf)
-               serialize(coeffs_chunk, coefs_file)
+               serialize(coeffs_chunk, coefs_file, ftype, nb_series_per_chunk)
                index = index + nb_series_per_chunk
                nb_curves = nb_curves + nrow(coeffs_chunk)
        }
        getCoefs = function(indices) getDataInFile(indices, coefs_file)
-######TODO: if DB, array rank --> ID at first retrieval, when computing coeffs; so:: NO use of IDs !
 
        if (nb_curves < min_series_per_chunk)
                stop("Not enough data: less rows than min_series_per_chunk!")
@@ -112,17 +112,36 @@ epclust = function(series,K1,K2,ntasks=1,nb_series_per_chunk=50*K1,min_series_pe
                upper_bound = ifelse( i<ntasks, min(nb_series_per_task*i,nb_curves), nb_curves )
                indices[((i-1)*nb_series_per_task+1):upper_bound]
        })
-       cl_tasks = parallel::makeCluster(ncores_tasks)
-       parallel::clusterExport(cl_tasks,
-               varlist=c("getSeries","getCoefs","K1","K2","WER","nb_series_per_chunk","ncores_clust"),
-               envir=environment())
+       cl = parallel::makeCluster(ncores_tasks)
        #1000*K1 (or K2) indices (or NOTHING--> series on file)
-       indices = parallel::parLapply(cl_tasks, indices_tasks, clusteringTask)
-       parallel::stopCluster(cl_tasks)
+       indices = unlist( parallel::parLapply(cl, indices_tasks, function(inds) {
+               clusteringTask(inds, getSeries, getSeries, getCoefs, K1, K2*(WER=="mix"),
+                       nb_series_per_chunk,ncores_clust,to_file=TRUE, ftype)
+       }) )
+       parallel::stopCluster(cl)
 
-       #Now series must be retrieved from synchrones_file, and have no ID
-       getSeries = function(indices, ids) getDataInFile(indices, synchrones_file)
+       getSeriesForSynchrones = getSeries
+       synchrones_file = paste(bin_dir,"synchrones",sep="")
+       if (WER=="mix")
+       {
+               indices = seq_len(ntasks*K2)
+               #Now series must be retrieved from synchrones_file
+               getSeries = function(inds) getDataInFile(inds, synchrones_file)
+               #Coefs must be re-computed
+               unlink(coefs_file)
+               index = 1
+               repeat
+               {
+                       series = getSeries((index-1)+seq_len(nb_series_per_chunk))
+                       if (is.null(series))
+                               break
+                       coeffs_chunk = curvesToCoeffs(series, wf)
+                       serialize(coeffs_chunk, coefs_file, ftype, nb_series_per_chunk)
+                       index = index + nb_series_per_chunk
+               }
+       }
 
        # Run step2 on resulting indices or series (from file)
-       computeClusters2(indices=if (WER=="end") indices else NULL, K2, to_file=FALSE)
+       clusteringTask(indices, getSeries, getSeriesForSynchrones, getCoefs, K1, K2,
+               nb_series_per_chunk, ncores_tasks*ncores_clust, to_file=FALSE, ftype)
 }