[R-sig-Geo] ENVI data and R

Wed Jul 30 09:15:08 CEST 2008

R is not intended for the analysis of large hyperspectral images.
If you are interested on spectra of selected pixels, just
import the envi spectra, I recall they are stored as if
they were envi images: a raw file + a text header file in which
you have all the info you need to import into R provided you have an 
elementary knowledge of R.

In general, the approach is using RS and/or GIS software to
select from the images the information that you really have to process 
in R, which is,
as stated by Roger, a tool for statistics.

Agus

Guy Serbin wrote:
> 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
>>
>>
> 
> 
> 

-- 
Dr. Agustin Lobo
Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
LLuis Sole Sabaris s/n
08028 Barcelona
Spain
Tel. 34 934095410
Fax. 34 934110012
email: Agustin.Lobo at ija.csic.es
http://www.ija.csic.es/gt/obster