[R-sig-Geo] ENVI data and R

Wed Jul 30 16:09:36 CEST 2008

Thank you for the information- I'll try that approach out.  The new
version of ENVI (4.5) is optimized to work with ArcGIS, so there may
be a way to pass spectra from ENVI to ArcGIS and then on to R if I
can't set up a direct ENVI/IDL to R connection.

I agree with you that R isn't for image processing (I certainly
enjoyed the two-three minute wait I had to endure to show a single
band ENVI image in R, something which would have been rendered
instantly in ENVI)- what we're interested in is using R for
statistical capabilities currently not available in either ENVI or
IDL.

Thanks for all your help,
Guy

On Wed, Jul 30, 2008 at 4:49 AM, Roger Bivand <Roger.Bivand at nhh.no> wrote:
> 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
>
>

-- 
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