[R-sig-Geo] problem reading hdf image
Matteo Mattiuzzi
matteo.mattiuzzi at boku.ac.at
Tue Oct 8 14:09:47 CEST 2013
Section 'Subdatasets'ie:
SUBDATASET_1_NAME=HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_b01
# this should work if R is in the HDF directory! if not redo gdalinfo with the file absolute path: gdalinfo /path/to/MOD09A1.A2011289.h11v11.005.2011298101214.hdf
r <- raster("HDF4_EOS:EOS_GRID:MOD09A1.A2011289.h11v11.005.2011298101214.hdf:MOD_Grid_500m_Surface_Reflectance:sur_refl_b01")
Take care about the quotation marks! You can do:
r <- raster("HDF4_EOS:EOS_GRID:MOD09A1.A2011289.h11v11.005.2011298101214.hdf:MOD_Grid_500m_Surface_Reflectance:sur_refl_b01") # removed
# or
r <- raster('HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_b01') # not removed
# The MODIS Package contains the function 'getSds' that extracts the SDS name, may you find something usable in there.
I hope this works as I am writing without testing!
Matteo
>>> Agustin Lobo <alobolistas at gmail.com> 10/08/13 1:45 PM >>>
Here it goes, thaks a lot for your help:
$ gdalinfo MOD09A1.A2011289.h11v11.005.2011298101214.hdf
Driver: HDF4/Hierarchical Data Format Release 4
Files: MOD09A1.A2011289.h11v11.005.2011298101214.hdf
Size is 512, 512
Coordinate System is `'
Metadata:
ASSOCIATEDINSTRUMENTSHORTNAME=MODIS
ASSOCIATEDPLATFORMSHORTNAME=Terra
ASSOCIATEDSENSORSHORTNAME=MODIS
AUTOMATICQUALITYFLAG=Passed
AUTOMATICQUALITYFLAGEXPLANATION=Always Passed
CHARACTERISTICBINANGULARSIZE250M=7.5
CHARACTERISTICBINANGULARSIZE500M=15.0
CHARACTERISTICBINSIZE250M=231.656358263889
CHARACTERISTICBINSIZE500M=463.312716527778
DATACOLUMNS250M=4800
DATACOLUMNS500M=2400
DATAROWS250M=4800
DATAROWS500M=2400
DAYNIGHTFLAG=Day
DESCRREVISION=5.1
EASTBOUNDINGCOORDINATE=-63.8417981939892
EQUATORCROSSINGDATE=2011-10-16
EQUATORCROSSINGDATE=2011-10-16
EQUATORCROSSINGDATE=2011-10-17
EQUATORCROSSINGDATE=2011-10-17
EQUATORCROSSINGDATE=2011-10-18
EQUATORCROSSINGDATE=2011-10-19
EQUATORCROSSINGDATE=2011-10-19
EQUATORCROSSINGDATE=2011-10-20
EQUATORCROSSINGDATE=2011-10-21
EQUATORCROSSINGDATE=2011-10-21
EQUATORCROSSINGDATE=2011-10-22
EQUATORCROSSINGDATE=2011-10-23
EQUATORCROSSINGDATE=2011-10-23
EQUATORCROSSINGLONGITUDE=-50.6540495500062
EQUATORCROSSINGLONGITUDE=-52.2073110490786
EQUATORCROSSINGLONGITUDE=-55.295882063234
EQUATORCROSSINGLONGITUDE=-58.3832333779475
EQUATORCROSSINGLONGITUDE=-61.4709999916156
EQUATORCROSSINGLONGITUDE=-66.1122213699271
EQUATORCROSSINGLONGITUDE=-69.2001737045505
EQUATORCROSSINGLONGITUDE=-72.2878369750113
EQUATORCROSSINGLONGITUDE=-75.3752441195227
EQUATORCROSSINGLONGITUDE=-76.9284675895243
EQUATORCROSSINGLONGITUDE=-80.0171825878646
EQUATORCROSSINGLONGITUDE=-83.1045607322162
EQUATORCROSSINGLONGITUDE=-86.1925733248845
EQUATORCROSSINGTIME=13:52:00.296015
EQUATORCROSSINGTIME=13:58:11.783455
EQUATORCROSSINGTIME=14:10:33.050881
EQUATORCROSSINGTIME=14:22:54.072603
EQUATORCROSSINGTIME=14:35:15.964468
EQUATORCROSSINGTIME=14:53:48.976317
EQUATORCROSSINGTIME=15:06:10.109374
EQUATORCROSSINGTIME=15:18:31.590110
EQUATORCROSSINGTIME=15:30:53.380135
EQUATORCROSSINGTIME=15:37:04.883419
EQUATORCROSSINGTIME=15:49:26.174422
EQUATORCROSSINGTIME=16:01:47.186363
EQUATORCROSSINGTIME=16:14:09.091656
EXCLUSIONGRINGFLAG=N
GEOANYABNORMAL=False
GEOESTMAXRMSERROR=50.0
GLOBALGRIDCOLUMNS250M=172800
GLOBALGRIDCOLUMNS500M=86400
GLOBALGRIDROWS250M=86400
GLOBALGRIDROWS500M=43200
GRANULEBEGINNINGDATETIME=2011-10-16T13:55:00.000000Z,
2011-10-17T14:40:00.000000Z, 2011-10-18T15:20:00.000000Z,
2011-10-19T14:25:00.000000Z, 2011-10-20T15:10:00.000000Z,
2011-10-21T14:15:00.000000Z, 2011-10-22T14:55:00.000000Z,
2011-10-23T14:00:00.000000Z
GRANULEDAYNIGHTFLAG=Day, Day, Day, Day, Day, Day, Day, Day
GRANULEDAYOFYEAR=289, 290, 291, 292, 293, 294, 295, 296
GRANULEENDINGDATETIME=2011-10-16T15:40:00.000000Z,
2011-10-17T16:25:00.000000Z, 2011-10-18T15:30:00.000000Z,
2011-10-19T16:10:00.000000Z, 2011-10-20T15:15:00.000000Z,
2011-10-21T16:00:00.000000Z, 2011-10-22T15:05:00.000000Z,
2011-10-23T15:50:00.000000Z
GRINGPOINTLATITUDE=-29.9999999973059, -19.900618521232,
-19.931832012974, -30.0325512403038
GRINGPOINTLONGITUDE=-80.8290376770946, -74.4810824411033,
-63.597163215181, -69.0095124954365
GRINGPOINTSEQUENCENO=1, 2, 3, 4
HDFEOSVersion=HDFEOS_V2.9
HORIZONTALTILENUMBER=11
INPUTPOINTER=MOD09GQ.A2011289.h11v11.005.2011291223308.hdf,
MOD09GQ.A2011290.h11v11.005.2011292054307.hdf,
MOD09GQ.A2011291.h11v11.005.2011293071509.hdf,
MOD09GQ.A2011292.h11v11.005.2011294224418.hdf,
MOD09GQ.A2011293.h11v11.005.2011295051850.hdf,
MOD09GQ.A2011294.h11v11.005.2011296053736.hdf,
MOD09GQ.A2011295.h11v11.005.2011297053810.hdf,
MOD09GQ.A2011296.h11v11.005.2011298095713.hdf,
MOD09GA.A2011289.h11v11.005.2011291223308.hdf,
MOD09GA.A2011290.h11v11.005.2011292054307.hdf,
MOD09GA.A2011291.h11v11.005.2011293071509.hdf,
MOD09GA.A2011292.h11v11.005.2011294224418.hdf,
MOD09GA.A2011293.h11v11.005.2011295051850.hdf,
MOD09GA.A2011294.h11v11.005.2011296053736.hdf,
MOD09GA.A2011295.h11v11.005.2011297053810.hdf,
MOD09GA.A2011296.h11v11.005.2011298095713.hdf
LOCALGRANULEID=MOD09A1.A2011289.h11v11.005.2011298101214.hdf
LOCALVERSIONID=5.0.11
LONGNAME=MODIS/Terra Surface Reflectance 8-Day L3 Global 500m SIN Grid
NADIRDATARESOLUTION250M=250m
NADIRDATARESOLUTION500M=500m
NORTHBOUNDINGCOORDINATE=-19.9999999982039
NUMBEROFGRANULES=8
NUMBEROFORBITS=13
ORBITNUMBER=62913
ORBITNUMBER=62914
ORBITNUMBER=62928
ORBITNUMBER=62929
ORBITNUMBER=62943
ORBITNUMBER=62957
ORBITNUMBER=62958
ORBITNUMBER=62972
ORBITNUMBER=62986
ORBITNUMBER=62987
ORBITNUMBER=63001
ORBITNUMBER=63015
ORBITNUMBER=63016
PARAMETERNAME=MOD09A1
PERCENTCLOUDY=15
PERCENTLAND=39
PERCENTLANDSEAMASKCLASS=1, 39, 0, 0, 0, 0, 0, 59
PERCENTLOWSUN=0
PERCENTPROCESSED=100
PERCENTSHADOW=4
PGEVERSION=5.0.11
PROCESSINGCENTER=MODAPS
PROCESSINGENVIRONMENT=Linux minion5550 2.6.18-274.3.1.el5PAE #1 SMP
Tue Sep 6 20:56:05 EDT 2011 i686 i686 i386 GNU/Linux
PROCESSVERSION=5.0.11
PRODUCTIONDATETIME=2011-10-25T10:12:15.000Z
QAPERCENTGOODQUALITY=95
QAPERCENTINTERPOLATEDDATA=0
QAPERCENTMISSINGDATA=0
QAPERCENTNOTPRODUCEDCLOUD=0
QAPERCENTNOTPRODUCEDOTHER=0
QAPERCENTOTHERQUALITY=4
QAPERCENTOUTOFBOUNDSDATA=0
QAPERCENTPOOROUTPUT500MBAND1=7
QAPERCENTPOOROUTPUT500MBAND2=20
QAPERCENTPOOROUTPUT500MBAND3=0
QAPERCENTPOOROUTPUT500MBAND4=0
QAPERCENTPOOROUTPUT500MBAND5=0
QAPERCENTPOOROUTPUT500MBAND6=0
QAPERCENTPOOROUTPUT500MBAND7=2
QUALITYCLASSPERCENTAGE500MBAND1=93, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 7, 0, 0
QUALITYCLASSPERCENTAGE500MBAND2=80, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 20, 0, 0
QUALITYCLASSPERCENTAGE500MBAND3=100, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0
QUALITYCLASSPERCENTAGE500MBAND4=100, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0
QUALITYCLASSPERCENTAGE500MBAND5=95, 0, 0, 0, 0, 0, 0, 5, 0, 0, 0, 0,
0, 0, 0, 0
QUALITYCLASSPERCENTAGE500MBAND6=100, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0
QUALITYCLASSPERCENTAGE500MBAND7=96, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 2, 2, 0
RANGEBEGINNINGDATE=2011-10-16
RANGEBEGINNINGTIME=00:00:00.000000
RANGEENDINGDATE=2011-10-23
RANGEENDINGTIME=23:59:59.000000
REPROCESSINGACTUAL=reprocessed
REPROCESSINGPLANNED=further update is anticipated
RESOLUTIONBANDS1AND2=500
SCIENCEQUALITYFLAG=Not Investigated
SCIENCEQUALITYFLAGEXPLANATION=See
http://landweb.nascom.nasa.gov/cgi-bin/QA_WWW/qaFlagPage.cgi?sat=terra
for the product Science Quality status.
SHORTNAME=MOD09A1
SOUTHBOUNDINGCOORDINATE=-29.9999999973059
SPSOPARAMETERS=2015
SYSTEMFILENAME=MOD09GQ.A2011289.h11v11.005.2011291223308.hdf,
MOD09GQ.A2011290.h11v11.005.2011292054307.hdf,
MOD09GQ.A2011291.h11v11.005.2011293071509.hdf,
MOD09GQ.A2011292.h11v11.005.2011294224418.hdf,
MOD09GQ.A2011293.h11v11.005.2011295051850.hdf,
MOD09GQ.A2011294.h11v11.005.2011296053736.hdf,
MOD09GQ.A2011295.h11v11.005.2011297053810.hdf,
MOD09GQ.A2011296.h11v11.005.2011298095713.hdf,
MOD09GA.A2011289.h11v11.005.2011291223308.hdf,
MOD09GA.A2011290.h11v11.005.2011292054307.hdf,
MOD09GA.A2011291.h11v11.005.2011293071509.hdf,
MOD09GA.A2011292.h11v11.005.2011294224418.hdf,
MOD09GA.A2011293.h11v11.005.2011295051850.hdf,
MOD09GA.A2011294.h11v11.005.2011296053736.hdf,
MOD09GA.A2011295.h11v11.005.2011297053810.hdf,
MOD09GA.A2011296.h11v11.005.2011298095713.hdf
TileID=51011011
VERSIONID=5
VERTICALTILENUMBER=11
WESTBOUNDINGCOORDINATE=-80.8290376770946
Subdatasets:
SUBDATASET_1_NAME=HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_b01
SUBDATASET_1_DESC=[2400x2400] sur_refl_b01
MOD_Grid_500m_Surface_Reflectance (16-bit integer)
SUBDATASET_2_NAME=HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_b02
SUBDATASET_2_DESC=[2400x2400] sur_refl_b02
MOD_Grid_500m_Surface_Reflectance (16-bit integer)
SUBDATASET_3_NAME=HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_b03
SUBDATASET_3_DESC=[2400x2400] sur_refl_b03
MOD_Grid_500m_Surface_Reflectance (16-bit integer)
SUBDATASET_4_NAME=HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_b04
SUBDATASET_4_DESC=[2400x2400] sur_refl_b04
MOD_Grid_500m_Surface_Reflectance (16-bit integer)
SUBDATASET_5_NAME=HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_b05
SUBDATASET_5_DESC=[2400x2400] sur_refl_b05
MOD_Grid_500m_Surface_Reflectance (16-bit integer)
SUBDATASET_6_NAME=HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_b06
SUBDATASET_6_DESC=[2400x2400] sur_refl_b06
MOD_Grid_500m_Surface_Reflectance (16-bit integer)
SUBDATASET_7_NAME=HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_b07
SUBDATASET_7_DESC=[2400x2400] sur_refl_b07
MOD_Grid_500m_Surface_Reflectance (16-bit integer)
SUBDATASET_8_NAME=HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_qc_500m
SUBDATASET_8_DESC=[2400x2400] sur_refl_qc_500m
MOD_Grid_500m_Surface_Reflectance (32-bit unsigned integer)
SUBDATASET_9_NAME=HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_szen
SUBDATASET_9_DESC=[2400x2400] sur_refl_szen
MOD_Grid_500m_Surface_Reflectance (16-bit integer)
SUBDATASET_10_NAME=HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_vzen
SUBDATASET_10_DESC=[2400x2400] sur_refl_vzen
MOD_Grid_500m_Surface_Reflectance (16-bit integer)
SUBDATASET_11_NAME=HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_raz
SUBDATASET_11_DESC=[2400x2400] sur_refl_raz
MOD_Grid_500m_Surface_Reflectance (16-bit integer)
SUBDATASET_12_NAME=HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_state_500m
SUBDATASET_12_DESC=[2400x2400] sur_refl_state_500m
MOD_Grid_500m_Surface_Reflectance (16-bit unsigned integer)
SUBDATASET_13_NAME=HDF4_EOS:EOS_GRID:"MOD09A1.A2011289.h11v11.005.2011298101214.hdf":MOD_Grid_500m_Surface_Reflectance:sur_refl_day_of_year
SUBDATASET_13_DESC=[2400x2400] sur_refl_day_of_year
MOD_Grid_500m_Surface_Reflectance (16-bit unsigned integer)
Corner Coordinates:
Upper Left ( 0.0, 0.0)
Lower Left ( 0.0, 512.0)
Upper Right ( 512.0, 0.0)
Lower Right ( 512.0, 512.0)
Center ( 256.0, 256.0)
On Tue, Oct 8, 2013 at 1:34 PM, Matteo Mattiuzzi
<matteo.mattiuzzi at boku.ac.at> wrote:
> Dear Agus,
>
> yes please send the output of gdalinfo (close to the end is the string you have to use).
>
>
> Matteo
>
>
>
>
>
>>>> Agustin Lobo <alobolistas at gmail.com> 10/07/13 5:42 PM >>>
> Hi!
>
> I get the following error when try to read an hdf image (release 4):
>
>> modisima <- stack(file.path(modisdir,"MOD09A1.A2011289.h11v11.005.2011298101214.hdf"))
> rgdal: version: 0.8-11, (SVN revision 479M)
> Geospatial Data Abstraction Library extensions to R successfully loaded
> Loaded GDAL runtime: GDAL 1.10.0, released 2013/04/24
> Path to GDAL shared files: /usr/share/gdal/1.10
> Loaded PROJ.4 runtime: Rel. 4.8.0, 6 March 2012, [PJ_VERSION: 480]
> Path to PROJ.4 shared files: (autodetected)
> Error in GDALinfo(filename, silent = silent, returnRAT = RAT,
> returnCategoryNames = RAT) :
> object 'RATlist' not found
> Error in .rasterObjectFromFile(x, objecttype = "RasterBrick", ...) :
> Cannot create a RasterLayer object from this file.
> In addition: Warning message:
> In dim(x) : no bands in dataset
>
> Also:
>
>> GDALinfo(file.path(modisdir,"MOD09A1.A2011289.h11v11.005.2011298101214.hdf"))
> Error in GDALinfo(file.path(modisdir,
> "MOD09A1.A2011289.h11v11.005.2011298101214.hdf")) :
> object 'scaleOffset' not found
> In addition: Warning messages:
> 1: In dim(x) : no bands in dataset
> 2: In GDALinfo(file.path(modisdir,
> "MOD09A1.A2011289.h11v11.005.2011298101214.hdf")) :
> GeoTransform values not available
>
> Nevertheless, hdf4 and 5 are listed by gdalDrivers() and, on the linux
> terminal, I do get
> output from gdalinfo (quite long, let me know if I should send it).
> Also, I can display the
> image in Qgis with no problem.
>
> Any idea on where the problem could be?
> Thanks,
> Agus
>
>> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8
> LC_PAPER=es_ES.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] rgdal_0.8-11 MODIS_0.10-8 raster_2.1-49 sp_1.0-13
>
> loaded via a namespace (and not attached):
> [1] grid_3.0.2 lattice_0.20-23 tools_3.0.2
>
> _______________________________________________
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>
>
>
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