[R-sig-Geo] ENVI data and R

Wed Jul 30 10:49:44 CEST 2008

On Tue, 29 Jul 2008, 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?

You can use R as a back-end compute engine through (D)COM, see:

http://cran.r-project.org/contrib/extra/dcom/

and note the scripting sample for Python. Regular (D)COM does arrays 
easily in VBA, going through usually Python means an extra copy, but may 
be more convenient. One needs to watch error trapping and what the 
different systems do with Inf, NaN, and NA values. I usually start from 
Python in front, and both Arc and R via (D)COM, but the Duke University 
MGET site has lots of code examples for interfacing R and Arc in 
different configurations:

http://code.env.duke.edu/projects/mget

MGET is under active development.

Roger

>
> 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
>>
>>
>
>
>
>

-- 
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