Antw: Re: HDF format

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.

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

     [[alternative HTML version deleted]]