[R] Reading a TIFF file

[Julio Rojas]

Thanks Uwe. I totally understood the problem. BTW, in your code you forgot to define "reduce". Can you define it in the function? If the file has different minimum as well as maximum levels from this one, will it work?

Regards.

Julio


--- El vie, 4/22/11, Uwe Ligges <ligges at statistik.tu-dortmund.de> escribió:

> De: Uwe Ligges <ligges at statistik.tu-dortmund.de>
> Asunto: Re: [R] Reading a TIFF file
> A: "Julio Rojas" <jcredberry at ymail.com>
> Cc: r-help at r-project.org
> Fecha: viernes, 22 de abril de 2011, 03:54 pm
> Fine, looking at the code shows that
> readTiff read the image with using libtiff which should be
> fine. Afterwards, a pixmap obnject is generated via 
> pixmapRGB() which includes the following lines:
> 
>     datamax <- max(data)
>     datamin <- min(data)
>     data <- as.numeric(data)
>     if (datamax > 1 || datamin < 0)
>         data <- (data -
> datamin)/(datamax - datamin)
> 
> That means the data is perfectly fitted into the [0,1]
> interval.
> 
> That means we have not only rescaled but also another 0
> now.
> 
> What I did is:
> 
> pic <- readTiff("test1_layer1.tif")
> pic <- pic at red
> ARC <- read.csv2("test1_arcgis.csv", header=TRUE)
> ARC <- matrix(ARC[,2], nrow=nrow(pic), byrow=TRUE)
> 
> plot(pic)
> plot(ARC)# looks *very* similar
> 
> plot(as.vector(pic) ~ as.vector(ARC))
> # all on one line
> 
> summary(lm(as.vector(pic) ~ as.vector(ARC)))
> # resuiduals < 10^(-14)
> 
> So the formula use to get from the ARC to the pixmap data
> is
> pixmapdata = -0.82278 * 0.01266 ARCdata
> 
> if you want to get the original data, you can adapt the
> readTiff function for your own use for greyscales (and save
> memory that way) as in:
> 
> 
> myReadTiff <- function (fn, page = 0)
> {
>   w <- .C("TiffGetWidth", as.character(fn), w =
> as.integer(0),
>     PACKAGE = "rtiff")$w
>   h <- .C("TiffGetHeight", as.character(fn), h =
> as.integer(0),
>     PACKAGE = "rtiff")$h
>   nw <- ceiling((1 - reduce) * w)
>   nh <- ceiling((1 - reduce) * h)
>   if (w > 0 && h > 0) {
>     tiff <- .C("TiffReadTIFFRGBA",
> as.character(fn),
>       page = as.integer(page),
>       r = integer(w * h), g = integer(w *
> h), b = integer(w * h),
>       PACKAGE = "rtiff")
>     tiff <- tiff$r / 255
>     tiff <- pixmapGrey(data = tiff, nrow = nh,
> ncol = nw)
>     return(tiff)
>   }
>   stop("Could not open", fn, ".  File corrupted
> or missing.\n")
> }
> 
> pic2 <- myReadTiff("test1_layer1.tif")
> 
> 
> Now pic2 at grey will be exactly the same as ARC/255 from
> above.
> 
> Uwe Ligges
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On 22.04.2011 15:10, Julio Rojas wrote:
> > Dear Uwe, find attached an small portion of the file
> I'm working with. ArcGIS values for this file are in the CSV
> file. They are a vector of all rows put together.
> > 
> > Thanks and regards.
> > 
> > 
> > --- El vie, 4/22/11, Uwe Ligges<ligges at statistik.tu-dortmund.de> 
> escribió:
> > 
> >> De: Uwe Ligges<ligges at statistik.tu-dortmund.de>
> >> Asunto: Re: [R] Reading a TIFF file
> >> A: "Julio Rojas"<jcredberry at ymail.com>
> >> Cc: r-help at r-project.org
> >> Fecha: viernes, 22 de abril de 2011, 12:37 pm
> >> Unless you can provide a small
> >> reproducible example (say a very small
> >> tiff including the values you got from the non-R
> software)
> >> it will be
> >> hard to tell what is going on.
> >> 
> >> Uwe Ligges
> >> 
> >> 
> >> On 22.04.2011 11:23, Julio Rojas wrote:
> >>> Dear all, I have been trying to speed up a
> process we
> >> have been done in ArcGIS. We have to read a single
> layer
> >> TIFF (monochrome image) in . For this, I have used
> the
> >> "rtiff" package. After reading the TIFF file, I
> compared the
> >> raw values for each pixel that I have in ArcGIS to
> the ones
> >> obtained in R. In ArcGIS I have discrete values in
> the range
> >> 0..255, while in R I have continuous values
> between 0..1.
> >> This, in itself might not be a problem if the
> values
> >> obtained in R, times 255 would show the values
> obtained in
> >> ArcGIS, but this is not the case. The images are
> very
> >> different. I tried to settle matters using
> Photoshop, and
> >> the values there are completely different from the
> other two
> >> (using RGB, the K value (in CMYK) or the B value
> (in
> >> HSB))!!!
> >>> 
> >>> Can somebody help me with this problem? Can I
> trust
> >> "rtiff"? Should I stick to a very slow process in
> ArcGIS?
> >> Why PS, which should be the perfect measuring
> stick, is
> >> showing another set of values?
> >>> 
> >>> Thanks in advance. Regards.
> >>> 
> >>> Julio
> >>> 
> >>>
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> >> 
>