## ----eval=FALSE----------------------------------------------------------
## source("http://bioconductor.org/biocLite.R")
## biocLite("gdsfmt")


## ----eval=FALSE----------------------------------------------------------
## library("devtools")
## install_github("zhengxwen/gdsfmt")


## ------------------------------------------------------------------------
library(gdsfmt)
gfile <- createfn.gds("test.gds")


## ----echo=FALSE----------------------------------------------------------
set.seed(1000)


## ------------------------------------------------------------------------
add.gdsn(gfile, "int", val=1:10000)
add.gdsn(gfile, "double", val=seq(1, 1000, 0.4))
add.gdsn(gfile, "character", val=c("int", "double", "logical", "factor"))
add.gdsn(gfile, "logical", val=rep(c(TRUE, FALSE, NA), 50), visible=FALSE)
add.gdsn(gfile, "factor", val=as.factor(c(NA, "AA", "CC")), visible=FALSE)
add.gdsn(gfile, "bit2", val=sample(0:3, 1000, replace=TRUE), storage="bit2")

# list and data.frame
add.gdsn(gfile, "list", val=list(X=1:10, Y=seq(1, 10, 0.25)))
add.gdsn(gfile, "data.frame", val=data.frame(X=1:19, Y=seq(1, 10, 0.5)))


## ------------------------------------------------------------------------
folder <- addfolder.gdsn(gfile, "folder")
add.gdsn(folder, "int", val=1:1000)
add.gdsn(folder, "double", val=seq(1, 100, 0.4), visible=FALSE)


## ------------------------------------------------------------------------
gfile


## ------------------------------------------------------------------------
print(gfile, all=TRUE)


## ------------------------------------------------------------------------
index.gdsn(gfile, "int")
index.gdsn(gfile, "list/Y")
index.gdsn(gfile, "folder/int")


## ------------------------------------------------------------------------
# close the GDS file
closefn.gds(gfile)


## ------------------------------------------------------------------------
gfile <- createfn.gds("test.gds")


## ------------------------------------------------------------------------
(n <- add.gdsn(gfile, "I1", val=matrix(1:15, nrow=3)))
read.gdsn(n)


## ------------------------------------------------------------------------
write.gdsn(n, rep(0,5), start=c(2,1), count=c(1,-1))
read.gdsn(n)


## ------------------------------------------------------------------------
append.gdsn(n, 16:24)
read.gdsn(n)


## ------------------------------------------------------------------------
(n2 <- add.gdsn(gfile, "I2", storage="int", valdim=c(100, 2000)))

for (i in 1:2000)
{
    write.gdsn(n2, seq.int(100*(i-1)+1, length.out=100),
        start=c(1,i), count=c(-1,1))
}


## ------------------------------------------------------------------------
(n3 <- add.gdsn(gfile, "I3", storage="int", valdim=c(100, 0), compress="ZIP"))

for (i in 1:2000)
{
    append.gdsn(n3, seq.int(100*(i-1)+1, length.out=100))
}

n3


## ------------------------------------------------------------------------
# close the GDS file
closefn.gds(gfile)


## ------------------------------------------------------------------------
gfile <- createfn.gds("test.gds")
add.gdsn(gfile, "I1", val=matrix(1:20, nrow=4))
add.gdsn(gfile, "I2", val=1:100)
closefn.gds(gfile)


## ------------------------------------------------------------------------
gfile <- openfn.gds("test.gds")
n <- index.gdsn(gfile, "I1")

read.gdsn(n)


## ------------------------------------------------------------------------
# read a subset
read.gdsn(n, start=c(2, 2), count=c(2, 3))


## ------------------------------------------------------------------------
# read a subset
readex.gdsn(n, list(c(FALSE,TRUE,TRUE,FALSE), c(TRUE,FALSE,TRUE,FALSE,TRUE)))


## ------------------------------------------------------------------------
apply.gdsn(n, margin=1, FUN=print, as.is="none")

apply.gdsn(n, margin=2, FUN=print, as.is="none")

# close the GDS file
closefn.gds(gfile)


## ------------------------------------------------------------------------
gfile <- createfn.gds("test.gds")
n1 <- add.gdsn(gfile, "I1", val=1:100)
n2 <- add.gdsn(gfile, "I2", val=matrix(1:20, nrow=4))

gfile


## ------------------------------------------------------------------------
fout <- file("text.txt", "wt")
apply.gdsn(n1, 1, FUN=cat, as.is="none", file=fout, fill=TRUE)
close(fout)

scan("text.txt")


## ------------------------------------------------------------------------
fout <- file("text.txt", "wt")
apply.gdsn(n2, 1, FUN=cat, as.is="none", file=fout, fill=32768)
close(fout)

readLines("text.txt")


## ------------------------------------------------------------------------
n.t <- add.gdsn(gfile, "transpose", storage="int", valdim=c(5,0))

# apply the function over rows of matrix
apply.gdsn(n2, margin=1, FUN=c, as.is="gdsnode", target.node=n.t)

# matrix transpose
read.gdsn(n.t)

# close the GDS file
closefn.gds(gfile)


## ------------------------------------------------------------------------
set.seed(1000)
val <- sample(seq(0,1,0.001), 50000, replace=TRUE)
head(val)

gfile <- createfn.gds("test.gds")

add.gdsn(gfile, "N1", val=val)
add.gdsn(gfile, "N2", val=val, compress="ZIP", closezip=TRUE)
add.gdsn(gfile, "N3", val=val, storage="float")
add.gdsn(gfile, "N4", val=val, storage="float", compress="ZIP", closezip=TRUE)
add.gdsn(gfile, "N5", val=val, storage="packedreal16", scale=0.001)
add.gdsn(gfile, "N6", val=val, storage="packedreal16", scale=0.001, compress="ZIP", closezip=TRUE)

gfile


## ----echo=FALSE----------------------------------------------------------
KB <- function(i)
{
    s <- objdesp.gdsn(index.gdsn(gfile, paste("N", i, sep="")))$size
    sprintf("%.1f KB", s/1000)
}

Ratio <- function(i)
{
    s <- objdesp.gdsn(index.gdsn(gfile, paste("N", i, sep="")))$size
    r <- 100*s / (8*length(val))
    sprintf("%.1f%%", r)
}

Epsilon <- function(i)
{
    ans <- mean(abs(val - read.gdsn(index.gdsn(gfile, paste0("N",i)))))
    sprintf("%0.3g", ans)
}


## ------------------------------------------------------------------------
# close the GDS file
closefn.gds(gfile)


## ----eval=FALSE----------------------------------------------------------
## set.seed(100)
## # 10,000,000 random 0,1 sequence of 32-bit integers
## v <- sample.int(2, 10*1000*1000, replace=TRUE) - 1L
## table(v)


## ----eval=FALSE----------------------------------------------------------
## # cteate a GDS file
## f <- createfn.gds("test.gds")
## 
## # compression algorithms
## compression <- c("", "ZIP.max", "ZIP_RA.max:16K", "LZ4.max", "LZ4_RA.max:16K")
## 
## # save
## for (i in 1:length(compression))
## 	print(add.gdsn(f, paste0("I", i), val=v, compress=compression[i], closezip=TRUE))
## 
## # close the file
## closefn.gds(f)


## ----eval=FALSE----------------------------------------------------------
## # open the GDS file
## f <- openfn.gds("test.gds")
## 
## # 10,000 random positions
## set.seed(1000)
## idx <- sample.int(length(v), 10000)
## 
## # for-loop each compression method
## for (i in 1:length(n))
## {
## 	cat("Compression:", compression[i], "\n")
## 	print(system.time({
## 		vv <- rep.int(0, length(idx))
## 		for (k in 1:length(idx))
## 			vv[k] <- read.gdsn(n[[i]], start=idx[k], count=1)
## 	}))
## }
## 
## # close the file
## closefn.gds(f)


## ------------------------------------------------------------------------
sessionInfo()


## ----echo=FALSE----------------------------------------------------------
unlink(c("test.gds", "text.txt"), force=TRUE)