[R-sig-Geo] Antw: Re: HDF format
Julian Zeidler
rlist at zeidlers.de
Thu Jan 26 16:04:04 CET 2012
Hi Vikram,
I think the Problem is inherent in rgdal /gdal under Windows.
On Linux gdalDrivers() shows (at least partial) support for HDF4 and HDF5
43 HDF4 Hierarchical Data Format Release 4
44 HDF4Image HDF4 Dataset
45 HDF5 Hierarchical Data Format Release 5
46 HDF5Image HDF5 Dataset
while they are missing from gdalDrivers() in Windows.
Therefore you should have more luck trying to get it to run under Linux
Best,
Julian
Am 26.01.2012 15:53, schrieb Matteo Mattiuzzi:
> ok should be simple...remove the space in: "c:/new aster" and try again
>
>>>> Vikram Ranga<babuawara at gmail.com> 1/26/2012 3:45 pm>>>
> OK I tried this,
> sds<-getSDS(HdfName="H:/new aster/AST_09_00304012003053127_20120124074826_13837.hdf")
> Warning message:
> running command 'C:\Windows\system32\cmd.exe /c gdalinfo H:/new aster/AST_09_00304012003053127_20120124074826_13837.hdf' had status 1
> but It is still returning NULL values...
>> sds
> $SDSnames
> NULL
>
> $SDS4gdal
> NULL
>
>
>
> On 1/26/2012 3:25 PM, Matteo Mattiuzzi wrote:
>
> Ok, I piked a ASTEfile: ftp://e4ftl01.cr.usgs.gov/ASTER_B/ASTT/AST_L1B.003/2000.03.30/AST_L1B_00303302000172133_20110111233757_1859.hdf
>
> # I am working on a Linux system I hope it does the same on Windows!!
>
> install.packages("MODIS", repos="http://R-Forge.R-project.org", dependencies=TRUE)
> library(MODIS)
>
> sds<- getSDS(HdfName= "/your/path/to/AST_L1B_00303302000172133_20110111233757_1859.hdf")
>
> SDS$SDS4gdal
> [1] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":VNIR_Swath:ImageData1"
> [2] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":VNIR_Swath:ImageData2"
> [3] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":VNIR_Swath:ImageData3N"
> [4] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":VNIR_Swath:ImageData3B"
> [5] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":SWIR_Swath:ImageData4"
> [6] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":SWIR_Swath:ImageData5"
> [7] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":SWIR_Swath:ImageData6"
> [8] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":SWIR_Swath:ImageData7"
> [9] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":SWIR_Swath:ImageData8"
> [10] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":SWIR_Swath:ImageData9"
> [11] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":TIR_Swath:ImageData10"
> [12] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":TIR_Swath:ImageData11"
> [13] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":TIR_Swath:ImageData12"
> [14] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":TIR_Swath:ImageData13"
> [15] "HDF4_EOS:EOS_SWATH:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":TIR_Swath:ImageData14"
> [16] "HDF4_SDS:UNKNOWN:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":0"
> [17] "HDF4_SDS:UNKNOWN:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":1"
> [18] "HDF4_SDS:UNKNOWN:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":2"
> [19] "HDF4_SDS:UNKNOWN:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":3"
> [20] "HDF4_SDS:UNKNOWN:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":4"
> [21] "HDF4_SDS:UNKNOWN:\"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf\":5"
> ...
>
>
> f1<- raster(SDS$SDS4gdal[1])
> Geospatial Data Abstraction Library extensions to R successfully loaded
> Loaded GDAL runtime: GDAL 1.8.0, released 2011/01/12
> Path to GDAL shared files: /usr/share/gdal/1.8
> Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009, [PJ_VERSION: 470]
> Path to PROJ.4 shared files: (autodetected)
> Warning messages:
> 1: In normalizePath(x) :
> path[1]="HDF4_EOS:EOS_SWATH:"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf":VNIR_Swath:ImageData1": No such file or directory
> 2: In .rasterFromGDAL(x, band = band, objecttype, ...) :
> GeoTransform values not available; georeferencing will not be correct
>> f1
> class : RasterLayer
> dimensions : 4200, 4980, 20916000 (nrow, ncol, ncell)
> resolution : 1, 1 (x, y)
> extent : 0, 4980, 0, 4200 (xmin, xmax, ymin, ymax)
> coord. ref. : NA
> values : HDF4_EOS:EOS_SWATH:"/home/matteo/Downloads/AST_L1B_00303302000172133_20110111233757_1859.hdf":VNIR_Swath:ImageData1
> min value : 0
> max value : 255
> # or
>
> f2<-stack(SDS$SDS4gdal[1:3])
> warning messages...
>
>> f2
> class : RasterStack
> dimensions : 4200, 4980, 20916000, 3 (nrow, ncol, ncell, nlayers)
> resolution : 1, 1 (x, y)
> extent : 0, 4980, 0, 4200 (xmin, xmax, ymin, ymax)
> coord. ref. : NA
> min values : 0 0 0
> max values : 255 255 255
>
> The file I have downloaded is a Swath product.... Spatial reference is lost and the data is NOT a GRIDDED file (Pixels are not squared but more polygons of different size). So you can't do many things you could do with an GRID File! ...Maybe you send me a link to download the file you are using (if you use d different type!)
>
> Matteo
>
>
>
>
>
>>>> Vikram Ranga<babuawara at gmail.com> ( mailto:babuawara at gmail.com ) 1/26/2012 2:55 pm>>>
> Hi Matteo,
> I am not sure about ASTER is HDF4 or HDF5.
> The codes you have given me I tried them
> sdsRaw<- shell(paste("gdalinfo ", HdfName,sep=""),intern=TRUE); this command seems to be working fine giving "Operable program or batch file ". And with raster(sdsRaw[1]) giving error : object 'SDSRaw' not found!
> While the another two codes does not seems to have worked
> SDSnames<- grep(x=sdsRaw,pattern="SUBDATASET_*.._NAME",value=T)
> The return with this command is character (0)
> SDSnames<- unlist(lapply(SDSnames,function(x) strsplit(x,"=")[[1]][2]))
> while with this one; the output is NULL.
>
> Though, I tried to install MODIS library to try getSDS() but could not find it in the library(strangely)
>
> Regards,
>
> Vikram.
>
> On 1/26/2012 11:29 AM, Matteo Mattiuzzi wrote:
>
>
> Hi Vikram,
>
> Isn't Aster HDF not an HDF4 format (like MODIS)? HDF4 and HDF5 are not really comparable/compatible each to other.
>
> If I'm right, you can open the file using GDAL, or even with the raster package, but you have to point the path to the layer (SDS) and not only to the file. There was a discussion between Robert Hijmans and Jan Verbesselt about that... https://r-forge.r-project.org/forum/message.php?msg_id=4132&group_id=294
>
> I think you can do the same with ASTER data.
>
> So now the only problem should be how to get the path to the SDS:
> in the MODIS package we use the function: getSDS(HdfName,method='gdal') , try to insert the full FILE-path in that function.
> Or you can try (on windows) with:
> sdsRaw<- shell(paste("gdalinfo ", HdfName,sep=""),intern=TRUE)
> SDSnames<- grep(x=sdsRaw,pattern="SUBDATASET_*.._NAME",value=T)
> SDSnames<- unlist(lapply(SDSnames,function(x) strsplit(x,"=")[[1]][2]))
>
> at least the sdsRaw should work...SDSnames I don't know, just test it (and maybe give me a short feedback)
>
> If everything runs fine you should be able to open in then raster package like that:
>
> SDS1<-raster(SDSnames[1]) # you can ignore the warning: normalizePath(x)
> or
> sds250<- stack(SDSnames[1:2]) # FOR MODIS! (only layers with the same resolution are 'stackable')
> ....
>
> Matteo
>
>
> So first you have to determinatate the full path to the SDS you wand to extract.
>
>>>> Vikram Ranga<babuawara at gmail.com> ( mailto:babuawara at gmail.com ) 26.01.12 10.20 Uhr>>>
> Hello Paul,
> sorry for abstruse mail. I am using R version 2.13.2 on windows (64
> bit). I am trying to open ASTER data files(*.hdf). Though, I tried few
> things like readGDAL() and raster() but got error message
> "53127_20120124074826_13837.hdf' not recognised as a supported file
> format" . I tried to load hdf5 package but while installing it I got
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) : package 'hdf5'
> is not available (for R version 2.13.2). I saw the discussion on hdf
> file on the list with topic "*What is the latest re: reading HDF files
> with R*". In the discussion Roger pointed out that building gdal
> against hdf format might help but I do not have a clue how to do that.
> let me know if you want more info from my end.
>
>
> Regards,
>
> Vikram.
>
> On 1/26/2012 10:01 AM, Paul Hiemstra wrote:
>> On 01/26/2012 08:53 AM, Vikram Ranga wrote:
>>> Hello List,
>>> I was trying to open HDF format files.
>>> Though I have followed the discussion on HDF5 format but really cant
>>> figure out as I tried to convert HDF to Geotiff but the tool is not
>>> working on my system. As the package is not for windows my options are
>>> very limited. Can anyone suggest me on this?
>>>
>>>
>>> Regards,
>>>
>>> Vikram.
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> R-sig-Geo at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>> Hi Vikram,
>>
>> You e-mail is much too vague to yield a good answer. A few questions
>> come to mind:
>>
>> - What is the structure of your HDF files
>> - What "discussion on hdf5 format" do you mean? And where can we find
>> it? It is best to give a summary in your mail what you took out of this
>> discussion.
>> - Show us concretely what you did (code, package etc). What R code
>> failed to load your HDF file, what was the error message it yielded?
>> - What version of R are you using, which package are you using to read
>> the HDF file, what are the versions of those packages. This can be
>> easily provided using the sessionInfo() command.
>>
>> Give us more to work with, or it will be very hard to help you.
>>
>> regards,
>> Paul
>>
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