On Sun, 18 Sep 2016, 19:04 Philippe de Rochambeau <phi...@free.fr> wrote:
> Please find below code that attempts to read ints, longs and floats from a
> binary file (which is a simplification of my original program).
> Please disregard the R inefficiencies, such as using rbind, for now.
> I’ve also included Java code to generate the binary file.
> The output shows that, at one point, anInt becomes undefined.
> Unfortunately, I couldn’t find the correct R function to determine whether
> inInt is undefined or not, as is.null, is.nan, and is.infinite don’t work.
> Any help would be much appreciated.
> Many thanks in advance.
> Philippe
>
> ———————
> [1] "anInt = 1"
> [1] "is.null FALSE"
> [1] "is.nan FALSE"
> [1] "is.infinite FALSE"
> [1] "aLong = 2"
> [1] "aFloat = 3.44440007209778"
> [1] "--------------------------"
> [1] "anInt = 2"
> [1] "is.null FALSE"
> [1] "is.nan FALSE"
> [1] "is.infinite FALSE"
> [1] "aLong = 22"
> [1] "aFloat = 13.4644002914429"
> [1] "--------------------------"
> [1] "anInt = 3"
> [1] "is.null FALSE"
> [1] "is.nan FALSE"
> [1] "is.infinite FALSE"
> [1] "aLong = 55"
> [1] "aFloat = 45.4444007873535"
> [1] "--------------------------"
> [1] "anInt = "
> [1] "is.null FALSE"
> [1] "is.nan "
> [1] "is.infinite "
> [1] "aLong = "
> [1] "aFloat = "
> [1] "--------------------------"
> [,1] [,2] [,3]
> [1,] 1 2 3.4444
> [2,] 2 22 13.4644
> [3,] 3 55 45.4444
> [4,] Integer,0 Integer,0 Numeric,0
> >
>
> -----------
>
>
> —————————————————————
>
> readFile <- function(inputPath) {
> URL <- file(inputPath, "rb")
> PLT <- matrix(nrow=0, ncol=3)
> counte <- 0
> max <- 4
> while (counte < max) {
> anInt <- readBin(con=URL, what=integer(), size=4, n=1, endian="big")
> print(paste("anInt =", anInt))
> #if (! (anInt == 0)) { print(paste("empty int")); break }
> print(paste("is.null ", is.null(anInt)))
> print(paste("is.nan ", is.nan(anInt)))
> print(paste("is.infinite ", is.infinite(anInt)))
> aLong <- readBin(URL, integer(), size=8, n=1, endian="big")
> print(paste("aLong =", aLong))
> aFloat <- readBin(URL, numeric(), size=4, n=1, endian="big")
> print(paste("aFloat =", aFloat))
> print("--------------------------")
> PLT <- rbind(PLT, list(anInt, aLong, aFloat))
> counte <- counte + 1
> } # end while
> close(URL)
> PLT
> }
> fichier <- "/Users/philippe/Desktop/datatests/data0.bin"
> PLT2 <- readFile(fichier)
> print(PLT2)
> —————————————————————
>
> import java.io.*;
>
> public class Main {
>
> Main() {
> writeData();
> }
>
> public static void main(String[] args) {
> new Main();
> }
>
> public void writeData() {
>
> final String path =
> "/Users/philippe/Desktop/datatests/data0.bin";
>
> DataOutputStream dos;
> try {
> dos = new DataOutputStream(new
> BufferedOutputStream(new FileOutputStream(path)));
> // big endian write! ("high byte first") , see
> https://docs.oracle.com/javase/7/docs/api/java/io/DataOutputStream.html
> dos.writeInt(1);
> dos.writeLong(2L);
> dos.writeFloat(3.4444F);
>
> dos.writeInt(2);
> dos.writeLong(22L);
> dos.writeFloat(13.4644F);
>
> dos.writeInt(3);
> dos.writeLong(55L);
> dos.writeFloat(45.4444F);
>
> dos.close();
> } catch (FileNotFoundException e) {
> e.printStackTrace();
> } catch (IOException ioe) {
> ioe.printStackTrace();
> }
>
> }
>
> }
>
>
> —————————————————————
>
>
>
>
>
>
> > Le 17 sept. 2016 à 20:45, Philippe de Rochambeau <phi...@free.fr> a
> écrit :
> >
> > Hi Jim,
> > this is exactly the answer I was look for. Many thanks. I didn’t R had a
> pack function, as in PERL.
> > To answer your earlier question, I am trying to update legacy code to
> read a binary file with unknown size, over a network, slice up it into rows
> each containing an integer, an integer, a long, a short, a float and a
> float, and stuff the rows into a matrix.
>
It's possible to read all rows fast as raw(), then parse in a vectorised
way with matrix indexing to group the bytes appropriately. There is an
example on the mailing list somewhere, but otherwise I can show an example
if that's of interest.
Cheers, Mike
> Best regards,
> > Philippe
> >
> >> Le 17 sept. 2016 à 20:38, jim holtman <jholt...@gmail.com <mailto:
> jholt...@gmail.com>> a écrit :
> >>
> >> Here is an example of how to do it:
> >>
> >> x <- 1:10 # integer values
> >> xf <- seq(1.0, 2, by = 0.1) # floating point
> >>
> >> setwd("d:/temp")
> >>
> >> # create file to write to
> >> output <- file('integer.bin', 'wb')
> >> writeBin(x, output) # write integer
> >> writeBin(xf, output) # write reals
> >> close(output)
> >>
> >>
> >> library(pack)
> >> library(readr)
> >>
> >> # read all the data at once
> >> allbin <- read_file_raw('integer.bin')
> >>
> >> # decode the data into a list
> >> (result <- unpack("V V V V V V V V V V d d d d d d d d d d", allbin))
> >>
> >>
> >>
> >>
> >> Jim Holtman
> >> Data Munger Guru
> >>
> >> What is the problem that you are trying to solve?
> >> Tell me what you want to do, not how you want to do it.
> >>
> >> On Sat, Sep 17, 2016 at 11:04 AM, Ismail SEZEN <sezenism...@gmail.com
> <mailto:sezenism...@gmail.com><mailto:sezenism...@gmail.com <mailto:
> sezenism...@gmail.com>>> wrote:
> >> I noticed same issue but didnt care much :)
> >>
> >> On Sat, Sep 17, 2016, 18:01 jim holtman <jholt...@gmail.com <mailto:
> jholt...@gmail.com> <mailto:jholt...@gmail.com <mailto:jholt...@gmail.com>>>
> wrote:
> >> Your example was not reproducible. Also how do you "break" out of the
> >> "while" loop?
> >>
> >>
> >> Jim Holtman
> >> Data Munger Guru
> >>
> >> What is the problem that you are trying to solve?
> >> Tell me what you want to do, not how you want to do it.
> >>
> >> On Sat, Sep 17, 2016 at 8:05 AM, Philippe de Rochambeau <phi...@free.fr
> <mailto:phi...@free.fr> <mailto:phi...@free.fr <mailto:phi...@free.fr>>>
> >> wrote:
> >>
> >>> Hello,
> >>> the following function, which stores numeric values extracted from a
> >>> binary file, into an R matrix, is very slow, especially when the said
> file
> >>> is several MB in size.
> >>> Should I rewrite the function in inline C or in C/C++ using Rcpp? If
> the
> >>> latter case is true, how do you « readBin » in Rcpp (I’m a total Rcpp
> >>> newbie)?
> >>> Many thanks.
> >>> Best regards,
> >>> phiroc
> >>>
> >>>
> >>> -------------
> >>>
> >>> # inputPath is something like http://myintranet/getData <
> http://myintranet/getData><http://myintranet/getData <
> http://myintranet/getData>>?
> >>> pathToFile=/usr/lib/xxx/yyy/data.bin <http://myintranet/getData <
> http://myintranet/getData> <http://myintranet/getData <
> http://myintranet/getData>>?
> >>> pathToFile=/usr/lib/xxx/yyy/data.bin>
> >>>
> >>> PLTreader <- function(inputPath){
> >>> URL <- file(inputPath, "rb")
> >>> PLT <- matrix(nrow=0, ncol=6)
> >>> compteurDePrints = 0
> >>> compteurDeLignes <- 0
> >>> maxiPrints = 5
> >>> displayData <- FALSE
> >>> while (TRUE) {
> >>> periodIndex <- readBin(URL, integer(), size=4, n=1,
> >>> endian="little") # int (4 bytes)
> >>> eventId <- readBin(URL, integer(), size=4, n=1,
> >>> endian="little") # int (4 bytes)
> >>> dword1 <- readBin(URL, integer(), size=4, signed=FALSE,
> >>> n=1, endian="little") # int
> >>> dword2 <- readBin(URL, integer(), size=4, signed=FALSE,
> >>> n=1, endian="little") # int
> >>> if (dword1 < 0) {
> >>> dword1 = dword1 + 2^32-1;
> >>> }
> >>> eventDate = (dword2*2^32 + dword1)/1000
> >>> repNum <- readBin(URL, integer(), size=2, n=1,
> >>> endian="little") # short (2 bytes)
> >>> exp <- readBin(URL, numeric(), size=4, n=1,
> >>> endian="little") # float (4 bytes, strangely enough, would expect 8)
> >>> loss <- readBin(URL, numeric(), size=4, n=1,
> >>> endian="little") # float (4 bytes)
> >>> PLT <- rbind(PLT, c(periodIndex, eventId, eventDate,
> >>> repNum, exp, loss))
> >>> } # end while
> >>> return(PLT)
> >>> close(URL)
> >>> }
> >>>
> >>> ----------------
> >>> [[alternative HTML version deleted]]
> >>>
> >>> ______________________________________________
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> >>
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> >>
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> >
> >
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> >
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> > PLEASE do read the posting guide
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--
Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia
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