[R-sig-Geo] RE : write NA with writeRaster

[Bastien Ferland-Raymond]

Hello Robert,

Thank you very much for your help, it's working perfectly with your code.

Thanks for the quick and complet answer

Bastien


________________________________________
De : Robert J. Hijmans [r.hijmans at gmail.com]
Date d'envoi : 9 novembre 2010 20:38
À : Bastien Ferland-Raymond
Cc : r-sig-geo at stat.math.ethz.ch
Objet : Re: [R-sig-Geo] write NA with writeRaster

Bastien,

The way it currently works with Byte type files is that all values
below zero become zero, and all values >= 255 become NA. That, is 255
is the "missing value flag"

What is clearly wrong, is that NA (and NaN) become zero, rather than
NA. I can solve this in raster, but it seems that is also a feature of
rgdal, where it could also be fixed.

Further, what you try here should not work. This to set the NA flag
for reading, not writing.
>  NAvalue(newRaster)<- NaN
To set the NA flag for writing (from raster version 1.6-16 and
onwards) you can use the argument NAflag=  in writeRaster (and other
functions that write files).

To use NaN as a NA flag is also questionable, because it is not really
a flag. It is (in most cases) equivalent, unless you want to
distinguish in your file between NaN and NA. And you can save NaN
values to disk with floating point values because you can store NaN
(invalid numbers) on disk. However, with byte values all you have is 8
bits and any combination is a valid number, so all you have is
0...255.

GeoTiff has "Internal nodata masks" that I have not explored. Not sure
if that will work (http://www.gdal.org/frmt_gtiff.html)

For now, this might work:

make.tiff <- function(NV=newValues,TT=Type,img=imgRaster,nom){
 pixelNDVIMatrix <- calculate_NDVI(TT,img,NV[c(1,2,3)])
 pixelNDVIMatrix[pixelNDVIMatrix == 255] <- 254
 pixelNDVIMatrix[is.na(pixelNDVIMatrix)] <- 255
 newRaster <- raster(pixelNDVIMatrix)
 NAvalue(newRaster)<- NaN
 nnom<-nom[NV[4]]
 writeRaster(newRaster, filename=nnom,datatype="INT1U",format="GTiff",
overwrite=FALSE)
}


Best, Robert


On Tue, Nov 9, 2010 at 8:46 AM, Bastien Ferland-Raymond
<bastien.ferland-raymond.1 at ulaval.ca> wrote:
> Dear R-user,
>
> I'm not new in R but I'm new dealing with images with R.  I checked over google and the help files of the Raster package but I couldn't find my answer.  Sorry if it's simple.
>
> I have a matrix 100x100 that I want to transfert into a tif image.  That's pretty easy with writeRaster, however I have some NaN in my image that I want to keep as NaN in the Tif image.
>
> Here is my code:
> ###
> make.tiff <- function(NV=newValues,TT=Type,img=imgRaster,nom){
>  pixelNDVIMatrix <- calculate_NDVI(TT,img,NV[c(1,2,3)])
>  newRaster <- raster(pixelNDVIMatrix)
>  NAvalue(newRaster)<- NaN
>  nnom<-nom[NV[4]]
>  writeRaster(newRaster, filename=nnom,datatype="INT1U",format="GTiff", overwrite=FALSE)
> }
> ###
>
> pixelNDVIMatrix is the matrix I want to make as tif.  It looks similar to:
>
>  NaN      NaN      NaN  177
> NaN       NaN      160    172
>  NaN      212       163      179
>  230       211        166       174
>
> In that example, the top left of the image in missing.  When I use writeRaster on that, it changes my NaN to 0, which is a problem.  Do you know how can I make the NaN bocome NODATA on the final image?
>
> My final objective is to create tif image in R that I would export to ENVI to calculate textural variables.  Having NODATA instead of 0 is important as I don't want ENVI to evaluate the texture of the "black" area created with the NODATA.  If tif image is the problem, I could probably change to another format.
>
> I'm using R 2.12 with the most recent packages
>
> Thanks for you help,
> Bastien Ferland-Raymond
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