I would gladly examine your example, Mike.
Cheers,
Philippe
> Le 18 sept. 2016 à 16:05, Michael Sumner <mdsum...@gmail.com> a écrit :
>
>
>
>> 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]]
>> >>>
>> >>> ______________________________________________
>> >>> R-help@r-project.org <mailto:R-help@r-project.org>
>> >>> <mailto:R-help@r-project.org <mailto:R-help@r-project.org>> mailing list
>> >>> -- To UNSUBSCRIBE and more, see
>> >>> https://stat.ethz.ch/mailman/listinfo/r-help
>> >>> <https://stat.ethz.ch/mailman/listinfo/r-help><https://stat.ethz.ch/mailman/listinfo/r-help
>> >>> <https://stat.ethz.ch/mailman/listinfo/r-help>>
>> >>> PLEASE do read the posting guide http://www.R-project.org/
>> >>> <http://www.r-project.org/> <http://www.r-project.org/
>> >>> <http://www.r-project.org/>>
>> >>> posting-guide.html
>> >>> and provide commented, minimal, self-contained, reproducible code.
>> >>
>> >> [[alternative HTML version deleted]]
>> >>
>> >> ______________________________________________
>> >> R-help@r-project.org <mailto:R-help@r-project.org>
>> >> <mailto:R-help@r-project.org <mailto:R-help@r-project.org>> mailing list
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>> >> <https://stat.ethz.ch/mailman/listinfo/r-help><https://stat.ethz.ch/mailman/listinfo/r-help
>> >> <https://stat.ethz.ch/mailman/listinfo/r-help>>
>> >> PLEASE do read the posting guide
>> >> http://www.R-project.org/posting-guide.html
>> >> <http://www.r-project.org/posting-guide.html>
>> >> <http://www.r-project.org/posting-guide.html
>> >> <http://www.r-project.org/posting-guide.html>>
>> >> and provide commented, minimal, self-contained, reproducible code.
>> >
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-help@r-project.org <mailto:R-help@r-project.org> mailing list -- To
>> > UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > <https://stat.ethz.ch/mailman/listinfo/r-help>
>> > PLEASE do read the posting guide
>> > http://www.R-project.org/posting-guide.html
>> > <http://www.r-project.org/posting-guide.html>
>> > and provide commented, minimal, self-contained, reproducible code.
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> --
> Dr. Michael Sumner
> Software and Database Engineer
> Australian Antarctic Division
> 203 Channel Highway
> Kingston Tasmania 7050 Australia
>
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