[H5r-commits] r33 - R inst

[noreply at r-forge.r-project.org]

Author: extemporaneousb
Date: 2010-06-15 17:28:46 +0200 (Tue, 15 Jun 2010)
New Revision: 33

Modified:
   R/h5R.R
   inst/performance.R
Log:
Performance Enhancements

Modified: R/h5R.R
===================================================================
--- R/h5R.R	2010-06-08 19:40:45 UTC (rev 32)
+++ R/h5R.R	2010-06-15 15:28:46 UTC (rev 33)
@@ -460,10 +460,17 @@
     } else {
       dim <- NA
     }
-    list(name = a[[1]], type = a[[2]], attributes = .listH5Attributes(h5Obj),
+    list(name = a[[1]],
+         type = a[[2]],
+         attributes = .listH5Attributes(h5Obj),
          dim = dim)
   })
   names(lst) <- sapply(lst, "[[", 1)
+  lst <- lapply(lst, function(a) {
+    a$name <- basename(a$name)
+    a
+  })
+
   return(lst)
 }
 

Modified: inst/performance.R
===================================================================
--- inst/performance.R	2010-06-08 19:40:45 UTC (rev 32)
+++ inst/performance.R	2010-06-15 15:28:46 UTC (rev 33)
@@ -10,38 +10,32 @@
 cDtas <- lapply(paste("cdata", chunks, sep = "_"), function(n) getH5Dataset(h5, n, inMemory = FALSE))
 names(cDtas) <- chunks
 
-N <- 1000
-K <- 1000
-
-f <- function(d, n = N, mu = 1000) {
+f <- function(d, n = 100, mu = 1000) {
   start <- runif(n, 1, length(d))
-  end  <- start + round(rexp(n, 1/mu))
-  end <- ifelse(end > length(d), start, end)
+  end   <- start + round(rexp(n, 1/mu))
+  end   <- ifelse(end > length(d), start, end)
+  width <- end - start + 1
   
-  mapply(function(s,e) {
-    z <- d[s:e]
-  }, start, end)
-
+  lapply(seq.int(1, n), function(i) {
+    readSlab(d, start[i], width[i])
+    return(NULL)
+  })
   return(TRUE)
 }
 
-g <- function(d, n = N, mu = 1000) {
-  start <- runif(n, 1, length(d))
-  end  <- start + round(rexp(n, 1/mu))
-  end <- ifelse(end > length(d), start, end)
-  
-  mapply(function(s,e) {
-    z <- d[matrix(c(s,e), ncol = 2)]
-  }, start, end)
+times <- replicate(100, {
+  system.time(f(cDtas[[1]], n = 1000))[3]
+})
 
-  return(TRUE)
-}
+pyTimes <- scan("pyres.txt")
 
-system.time(f(cDtas[[1]], n = 100000))
-system.time(g(cDtas[[1]], n = 100000))
+png("numpyVR.png")
+par(mar = c(8, 6, 5, 1), cex.lab = 2, cex.axis = 2, cex.main = 2)
+boxplot(list("Python" = pyTimes, "R" = times), ylim = c(.075, .15),
+        las = 2, main = "Random 1k dataset slice")
+dev.off()
 
 
-
 Rprof("rprof")
 levelplot(x <- do.call(rbind, lapply(cDtas, function(a) {
   set.seed(10)