[R-sig-Geo] ENVI data and R

[Guy Serbin]

My machine currently has 4 GB on it, but a lot of that's getting eaten
by video memory and the other programs I have in memory.  Also, some
of my image cubes are 12 GB in size, so I'd need to find a workaround
anyways.  However, since what my colleagues and I are interested in
are pixel-by-pixel spectral analyses, I assume the best approach would
be to pass the spectra either from ENVI/IDL (for which there is no
frontend, but I have logged a request with ITT Visual Solutions to
develop one) or conversely from ArcGIS (which can read ENVI data with
the ENVI Reader) into R for analysis.

Are you aware of ways to send arrays back and forth between R and ArcGIS?

Guy

On Tue, Jul 29, 2008 at 4:24 PM, Roger Bivand <Roger.Bivand at nhh.no> wrote:
> On Tue, 29 Jul 2008, Guy Serbin wrote:
>
>> Thank you all for the help- I successfully read an image into R using
>> these methods.
>>
>> I did, however, encounter some problems when loading a hyperspectral
>> image cube into R as it was unable to allocate the 2.9 GB of volatile
>> memory that it needed.
>
> Buy more memory, 64-bit Linux works fine. Seriously, R is for statistics, so
> its memory management is designed for samples, even though very large
> samples can be handled when used appropriately. If your data are in a
> GeoTiff, you can read them by band using functions in the rgdal package, or
> equally well many bands in a window or tile of a larger scene. Note that
> ArcGIS uses GDAL too for handling some raster formats. Using R does mean
> thinking through your work flow.
>
> Roger
>
>>
>> Is there a way to improve memory management by R, so that it only
>> reads in the data when actually needed for processing, e.g., only read
>> in the bands I need, or conversely read in spectra on a per-pixel
>> basis?
>>
>> Guy
>>
>> On Tue, Jul 29, 2008 at 4:05 PM, PUJAN RAJ REGMI
>> <regmi_pujan at hotmail.com> wrote:
>>>
>>> This might help to mange the orientation of image:
>>>
>>> # To read ENVI format
>>> cir.image<-("YOUR_ENVI_FILE")
>>> CIR.envi<-read.ENVI(cir.image,headerfile=paste(cir.image,".hdr",sep=""))
>>> # To Show image
>>> CIR.envi.band1<-CIR.envi[,,1]
>>> CIR.envi.band1.s<-CIR.envi.band1[order(nrow(CIR.envi.band1):1),]
>>> CIR.envi.band1.t<-t(CIR.envi.band1.s)
>>> image(CIR.envi.band1.t,main="")
>>> mtext("Raw Matrix ENVI Image for Band1", side=3,line=2, font=3,cex=1.25)
>>>
>>> Pujan
>>> ________________________________
>>>>
>>>> From: andrew.niccolai at yale.edu
>>>> To: guy.serbin at gmail.com; R-sig-Geo at stat.math.ethz.ch
>>>> Date: Tue, 29 Jul 2008 14:24:04 -0400
>>>> Subject: Re: [R-sig-Geo] ENVI data and R
>>>>
>>>> This code might help:
>>>>
>>>>
>>>>
>>>> ############################################################################
>>>> ####
>>>>
>>>>
>>>> ############################################################################
>>>> ####
>>>> ## Read in envi file
>>>> cir.image <- "C:/YOUR_ENVI_FILE"
>>>> CIR.envi = read.ENVI(cir.image, headerfile=paste(cir.image,".hdr",
>>>> sep=""))
>>>>
>>>>
>>>>
>>>> ############################################################################
>>>> ####
>>>>
>>>>
>>>> ############################################################################
>>>> ####
>>>> ## Show image
>>>> CIR.envi.band1 <- CIR.envi[,,1]
>>>> image(CIR.envi.band1, main="")
>>>> mtext("Raw Matrix ENVI Image for Band 1", side=3,line = 2, font=3,
>>>> cex=1.25)
>>>>
>>>>
>>>>
>>>> ############################################################################
>>>> ####
>>>>
>>>>
>>>> ############################################################################
>>>> ####
>>>>
>>>> Andrew Niccolai
>>>> Doctoral Candidate
>>>> Yale School of Forestry
>>>>
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: r-sig-geo-bounces at stat.math.ethz.ch
>>>> [mailto:r-sig-geo-bounces at stat.math.ethz.ch] On Behalf Of Guy Serbin
>>>> Sent: Tuesday, July 29, 2008 12:55 PM
>>>> To: R-sig-Geo at stat.math.ethz.ch
>>>> Subject: [R-sig-Geo] ENVI data and R
>>>>
>>>> Hi,
>>>>
>>>> I was wondering if anyone knows how to either call up R functions from
>>>> within IDL, or conversely read ENVI image data into R. If you have
>>>> any advice I'd greatly appreciate it.
>>>>
>>>> Thanks,
>>>> Guy Serbin
>>>>
>>>> --
>>>> Guy Serbin, Ph.D.
>>>> Research Soil Scientist
>>>> Hydrology and Remote Sensing Lab
>>>> Bldg 007 Rm 104 BARC-West
>>>> 10300 Baltimore Blvd
>>>> Beltsville, MD 20705-2350 USA
>>>> +1(301)504-5250 guy.serbin at gmail.com
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> R-sig-Geo at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> R-sig-Geo at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>> ________________________________
>>> Stay in touch when you're away with Windows Live Messenger. IM anytime
>>> you're online.
>>
>>
>>
>>
>
> --
> Roger Bivand
> Economic Geography Section, Department of Economics, Norwegian School of
> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
> e-mail: Roger.Bivand at nhh.no
>
>



-- 
Guy Serbin, Ph.D.
Research Soil Scientist
Hydrology and Remote Sensing Lab
Bldg 007 Rm 104 BARC-West
10300 Baltimore Blvd
Beltsville, MD 20705-2350 USA
+1(301)504-5250 guy.serbin at gmail.com