Problem reading a HDF5 file with readGDAL in Windows

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Problem reading a HDF5 file with readGDAL in Windows

Oscar Perpiñan-2
Hello,

I am trying to read a HDF5 file whose variable name contains '//'. I have no
problem in a Linux machine, but 'readGDAL' throws an error in Windows. If I
am not wrong, it is because the initialize method of the 'GDALReadOnlyDataset'
class includes a call to 'normalizePath'.

For example, the next code works in Linux but fails in Windows (it uses this
file
ftp://atrain.sci.gsfc.nasa.gov/data/s4pa//OMI/OMCLDO2_CPR.003/2015/125/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5
)

x <- readGDAL("HDF5:OMI.L2.CloudOMCLDO2Strip200kmAlongClo
udSat.2015.05.05.020752Z.v003.he5://HDFEOS/SWATHS/
CloudFractionAndPressure/Data_Fields/ChiSquaredOfFit")

Is there any way to circumvent this problem?

Thanks in advance.

Oscar.
-----------------------------------------------------------------
Oscar Perpiñán Lamigueiro
Dpto. Ing. Eléctrica, Electrónica, Automática y Física Aplicada (ETSIDI-UPM)
Grupo de Sistemas Fotovoltaicos (IES-UPM)
URL: http://oscarperpinan.github.io

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Re: Problem reading a HDF5 file with readGDAL in Windows

Michael Sumner-2
Are you sure you have the HDF5 driver in Windows?  Do you build yourself
against your own GDAL or against OSGeo4W?  (It's not in the CRAN
windows-build).

This is the error the CRAN build gives (though it's actually not
recognizing the driver):

"... does not exist in the file system, and is not recognised as a
supported dataset name."

(gdalinfo works fine with your subdataset string here on my Windows8 with
OSGeo4W. )

Cheers, Mike.




On Tue, 5 May 2015 at 21:35 Oscar Perpiñan <[hidden email]> wrote:

> Hello,
>
> I am trying to read a HDF5 file whose variable name contains '//'. I have
> no
> problem in a Linux machine, but 'readGDAL' throws an error in Windows. If I
> am not wrong, it is because the initialize method of the
> 'GDALReadOnlyDataset'
> class includes a call to 'normalizePath'.
>
> For example, the next code works in Linux but fails in Windows (it uses
> this
> file
>
> ftp://atrain.sci.gsfc.nasa.gov/data/s4pa//OMI/OMCLDO2_CPR.003/2015/125/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5
> )
>
> x <- readGDAL("HDF5:OMI.L2.CloudOMCLDO2Strip200kmAlongClo
> udSat.2015.05.05.020752Z.v003.he5://HDFEOS/SWATHS/
> CloudFractionAndPressure/Data_Fields/ChiSquaredOfFit")
>
> Is there any way to circumvent this problem?
>
> Thanks in advance.
>
> Oscar.
> -----------------------------------------------------------------
> Oscar Perpiñán Lamigueiro
> Dpto. Ing. Eléctrica, Electrónica, Automática y Física Aplicada
> (ETSIDI-UPM)
> Grupo de Sistemas Fotovoltaicos (IES-UPM)
> URL: http://oscarperpinan.github.io
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

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Re: Problem reading a HDF5 file with readGDAL in Windows

John Baumgartner
In reply to this post by Oscar Perpiñan-2
Not a remedy, but the following might be a workable alternative...

ncdf4::nc_open("OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5")$var$`Data
Fields/ChiSquaredOfFit`

I'm not familiar with HDF5 structure, so not sure of possible downsides.

Cheers,
John

On Tue, May 5, 2015 at 9:34 PM, Oscar Perpiñan <[hidden email]>
wrote:

> Hello,
>
> I am trying to read a HDF5 file whose variable name contains '//'. I have
> no
> problem in a Linux machine, but 'readGDAL' throws an error in Windows. If I
> am not wrong, it is because the initialize method of the
> 'GDALReadOnlyDataset'
> class includes a call to 'normalizePath'.
>
> For example, the next code works in Linux but fails in Windows (it uses
> this
> file
>
> ftp://atrain.sci.gsfc.nasa.gov/data/s4pa//OMI/OMCLDO2_CPR.003/2015/125/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5
> )
>
> x <- readGDAL("HDF5:OMI.L2.CloudOMCLDO2Strip200kmAlongClo
> udSat.2015.05.05.020752Z.v003.he5://HDFEOS/SWATHS/
> CloudFractionAndPressure/Data_Fields/ChiSquaredOfFit")
>
> Is there any way to circumvent this problem?
>
> Thanks in advance.
>
> Oscar.
> -----------------------------------------------------------------
> Oscar Perpiñán Lamigueiro
> Dpto. Ing. Eléctrica, Electrónica, Automática y Física Aplicada
> (ETSIDI-UPM)
> Grupo de Sistemas Fotovoltaicos (IES-UPM)
> URL: http://oscarperpinan.github.io
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

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Re: Problem reading a HDF5 file with readGDAL in Windows

Robert Hijmans
In which case you can change the extension to '.nc' and do

library(raster)
library(ncdf4)
x <- raster("E:/downloads/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.nc",
var='Data Fields/ChiSquaredOfFit')

Robert

On Tue, May 5, 2015 at 5:28 AM, John Baumgartner <[hidden email]> wrote:

> Not a remedy, but the following might be a workable alternative...
>
> ncdf4::nc_open("OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5")$var$`Data
> Fields/ChiSquaredOfFit`
>
> I'm not familiar with HDF5 structure, so not sure of possible downsides.
>
> Cheers,
> John
>
> On Tue, May 5, 2015 at 9:34 PM, Oscar Perpiñan <[hidden email]>
> wrote:
>
>> Hello,
>>
>> I am trying to read a HDF5 file whose variable name contains '//'. I have
>> no
>> problem in a Linux machine, but 'readGDAL' throws an error in Windows. If I
>> am not wrong, it is because the initialize method of the
>> 'GDALReadOnlyDataset'
>> class includes a call to 'normalizePath'.
>>
>> For example, the next code works in Linux but fails in Windows (it uses
>> this
>> file
>>
>> ftp://atrain.sci.gsfc.nasa.gov/data/s4pa//OMI/OMCLDO2_CPR.003/2015/125/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5
>> )
>>
>> x <- readGDAL("HDF5:OMI.L2.CloudOMCLDO2Strip200kmAlongClo
>> udSat.2015.05.05.020752Z.v003.he5://HDFEOS/SWATHS/
>> CloudFractionAndPressure/Data_Fields/ChiSquaredOfFit")
>>
>> Is there any way to circumvent this problem?
>>
>> Thanks in advance.
>>
>> Oscar.
>> -----------------------------------------------------------------
>> Oscar Perpiñán Lamigueiro
>> Dpto. Ing. Eléctrica, Electrónica, Automática y Física Aplicada
>> (ETSIDI-UPM)
>> Grupo de Sistemas Fotovoltaicos (IES-UPM)
>> URL: http://oscarperpinan.github.io
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo

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Re: Problem reading a HDF5 file with readGDAL in Windows

Robert Hijmans
Even better (renaming not necessary):

x <- raster("E:/downloads/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5",
var='Data Fields/ChiSquaredOfFit', ncdf=TRUE)

Best, Robert

On Tue, May 5, 2015 at 10:24 AM, Robert J. Hijmans <[hidden email]> wrote:

> In which case you can change the extension to '.nc' and do
>
> library(raster)
> library(ncdf4)
> x <- raster("E:/downloads/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.nc",
> var='Data Fields/ChiSquaredOfFit')
>
> Robert
>
> On Tue, May 5, 2015 at 5:28 AM, John Baumgartner <[hidden email]> wrote:
>> Not a remedy, but the following might be a workable alternative...
>>
>> ncdf4::nc_open("OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5")$var$`Data
>> Fields/ChiSquaredOfFit`
>>
>> I'm not familiar with HDF5 structure, so not sure of possible downsides.
>>
>> Cheers,
>> John
>>
>> On Tue, May 5, 2015 at 9:34 PM, Oscar Perpiñan <[hidden email]>
>> wrote:
>>
>>> Hello,
>>>
>>> I am trying to read a HDF5 file whose variable name contains '//'. I have
>>> no
>>> problem in a Linux machine, but 'readGDAL' throws an error in Windows. If I
>>> am not wrong, it is because the initialize method of the
>>> 'GDALReadOnlyDataset'
>>> class includes a call to 'normalizePath'.
>>>
>>> For example, the next code works in Linux but fails in Windows (it uses
>>> this
>>> file
>>>
>>> ftp://atrain.sci.gsfc.nasa.gov/data/s4pa//OMI/OMCLDO2_CPR.003/2015/125/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5
>>> )
>>>
>>> x <- readGDAL("HDF5:OMI.L2.CloudOMCLDO2Strip200kmAlongClo
>>> udSat.2015.05.05.020752Z.v003.he5://HDFEOS/SWATHS/
>>> CloudFractionAndPressure/Data_Fields/ChiSquaredOfFit")
>>>
>>> Is there any way to circumvent this problem?
>>>
>>> Thanks in advance.
>>>
>>> Oscar.
>>> -----------------------------------------------------------------
>>> Oscar Perpiñán Lamigueiro
>>> Dpto. Ing. Eléctrica, Electrónica, Automática y Física Aplicada
>>> (ETSIDI-UPM)
>>> Grupo de Sistemas Fotovoltaicos (IES-UPM)
>>> URL: http://oscarperpinan.github.io
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo

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Re: Problem reading a HDF5 file with readGDAL in Windows

Michael Sumner-2
On Wed, 6 May 2015 at 03:28 Robert J. Hijmans <[hidden email]> wrote:

> Even better (renaming not necessary):
>
> x <-
> raster("E:/downloads/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5",
> var='Data Fields/ChiSquaredOfFit', ncdf=TRUE)
>
> Best, Robert
>


But only if you build and install ncdf4 yourself (or use DP's one off-CRAN:
http://cirrus.ucsd.edu/~pierce/ncdf/)

There's no ncdf4 for Windows on CRAN.

Robert's solution doesn't work for me on Windows with ncdf (though I am
sure it it would if I build ncdf with NetCDF4).

(I feel like I've missed something here . . .)

Cheers, Mike.


>
> On Tue, May 5, 2015 at 10:24 AM, Robert J. Hijmans <[hidden email]>
> wrote:
> > In which case you can change the extension to '.nc' and do
> >
> > library(raster)
> > library(ncdf4)
> > x <- raster("E:/downloads/
> OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.nc",
> > var='Data Fields/ChiSquaredOfFit')
> >
> > Robert
> >
> > On Tue, May 5, 2015 at 5:28 AM, John Baumgartner <[hidden email]>
> wrote:
> >> Not a remedy, but the following might be a workable alternative...
> >>
> >>
> ncdf4::nc_open("OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5")$var$`Data
> >> Fields/ChiSquaredOfFit`
> >>
> >> I'm not familiar with HDF5 structure, so not sure of possible downsides.
> >>
> >> Cheers,
> >> John
> >>
> >> On Tue, May 5, 2015 at 9:34 PM, Oscar Perpiñan <
> [hidden email]>
> >> wrote:
> >>
> >>> Hello,
> >>>
> >>> I am trying to read a HDF5 file whose variable name contains '//'. I
> have
> >>> no
> >>> problem in a Linux machine, but 'readGDAL' throws an error in Windows.
> If I
> >>> am not wrong, it is because the initialize method of the
> >>> 'GDALReadOnlyDataset'
> >>> class includes a call to 'normalizePath'.
> >>>
> >>> For example, the next code works in Linux but fails in Windows (it uses
> >>> this
> >>> file
> >>>
> >>>
> ftp://atrain.sci.gsfc.nasa.gov/data/s4pa//OMI/OMCLDO2_CPR.003/2015/125/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5
> >>> )
> >>>
> >>> x <- readGDAL("HDF5:OMI.L2.CloudOMCLDO2Strip200kmAlongClo
> >>> udSat.2015.05.05.020752Z.v003.he5://HDFEOS/SWATHS/
> >>> CloudFractionAndPressure/Data_Fields/ChiSquaredOfFit")
> >>>
> >>> Is there any way to circumvent this problem?
> >>>
> >>> Thanks in advance.
> >>>
> >>> Oscar.
> >>> -----------------------------------------------------------------
> >>> Oscar Perpiñán Lamigueiro
> >>> Dpto. Ing. Eléctrica, Electrónica, Automática y Física Aplicada
> >>> (ETSIDI-UPM)
> >>> Grupo de Sistemas Fotovoltaicos (IES-UPM)
> >>> URL: http://oscarperpinan.github.io
> >>>
> >>>         [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> R-sig-Geo mailing list
> >>> [hidden email]
> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>>
> >>
> >>         [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> R-sig-Geo mailing list
> >> [hidden email]
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

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Re: Problem reading a HDF5 file with readGDAL in Windows

Robert Hijmans
Yes, you need the ncdf4 package (apart from build your own options
that I would not generally recommend). That's why I explicitly did
`library(ncdf4)`. On windows that indeed means downloading it from
http://cirrus.ucsd.edu/~pierce/ncdf/ and unzipping the content to the
right folder ("install from local zip file" in Rgui). Just a tiny bit
of additional effort.

Robert

On Tue, May 5, 2015 at 2:20 PM, Michael Sumner <[hidden email]> wrote:

>
>
> On Wed, 6 May 2015 at 03:28 Robert J. Hijmans <[hidden email]> wrote:
>>
>> Even better (renaming not necessary):
>>
>> x <-
>> raster("E:/downloads/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5",
>> var='Data Fields/ChiSquaredOfFit', ncdf=TRUE)
>>
>> Best, Robert
>
>
>
> But only if you build and install ncdf4 yourself (or use DP's one off-CRAN:
> http://cirrus.ucsd.edu/~pierce/ncdf/)
>
> There's no ncdf4 for Windows on CRAN.
>
> Robert's solution doesn't work for me on Windows with ncdf (though I am sure
> it it would if I build ncdf with NetCDF4).
>
> (I feel like I've missed something here . . .)
>
> Cheers, Mike.
>
>>
>>
>> On Tue, May 5, 2015 at 10:24 AM, Robert J. Hijmans <[hidden email]>
>> wrote:
>> > In which case you can change the extension to '.nc' and do
>> >
>> > library(raster)
>> > library(ncdf4)
>> > x <-
>> > raster("E:/downloads/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.nc",
>> > var='Data Fields/ChiSquaredOfFit')
>> >
>> > Robert
>> >
>> > On Tue, May 5, 2015 at 5:28 AM, John Baumgartner <[hidden email]>
>> > wrote:
>> >> Not a remedy, but the following might be a workable alternative...
>> >>
>> >>
>> >> ncdf4::nc_open("OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5")$var$`Data
>> >> Fields/ChiSquaredOfFit`
>> >>
>> >> I'm not familiar with HDF5 structure, so not sure of possible
>> >> downsides.
>> >>
>> >> Cheers,
>> >> John
>> >>
>> >> On Tue, May 5, 2015 at 9:34 PM, Oscar Perpiñan
>> >> <[hidden email]>
>> >> wrote:
>> >>
>> >>> Hello,
>> >>>
>> >>> I am trying to read a HDF5 file whose variable name contains '//'. I
>> >>> have
>> >>> no
>> >>> problem in a Linux machine, but 'readGDAL' throws an error in Windows.
>> >>> If I
>> >>> am not wrong, it is because the initialize method of the
>> >>> 'GDALReadOnlyDataset'
>> >>> class includes a call to 'normalizePath'.
>> >>>
>> >>> For example, the next code works in Linux but fails in Windows (it
>> >>> uses
>> >>> this
>> >>> file
>> >>>
>> >>>
>> >>> ftp://atrain.sci.gsfc.nasa.gov/data/s4pa//OMI/OMCLDO2_CPR.003/2015/125/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5
>> >>> )
>> >>>
>> >>> x <- readGDAL("HDF5:OMI.L2.CloudOMCLDO2Strip200kmAlongClo
>> >>> udSat.2015.05.05.020752Z.v003.he5://HDFEOS/SWATHS/
>> >>> CloudFractionAndPressure/Data_Fields/ChiSquaredOfFit")
>> >>>
>> >>> Is there any way to circumvent this problem?
>> >>>
>> >>> Thanks in advance.
>> >>>
>> >>> Oscar.
>> >>> -----------------------------------------------------------------
>> >>> Oscar Perpiñán Lamigueiro
>> >>> Dpto. Ing. Eléctrica, Electrónica, Automática y Física Aplicada
>> >>> (ETSIDI-UPM)
>> >>> Grupo de Sistemas Fotovoltaicos (IES-UPM)
>> >>> URL: http://oscarperpinan.github.io
>> >>>
>> >>>         [[alternative HTML version deleted]]
>> >>>
>> >>> _______________________________________________
>> >>> R-sig-Geo mailing list
>> >>> [hidden email]
>> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>> >>>
>> >>
>> >>         [[alternative HTML version deleted]]
>> >>
>> >> _______________________________________________
>> >> R-sig-Geo mailing list
>> >> [hidden email]
>> >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>> _______________________________________________
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>> [hidden email]
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Re: Problem reading a HDF5 file with readGDAL in Windows

Oscar Perpiñan-2
In reply to this post by Michael Sumner-2
Hi,


> Are you sure you have the HDF5 driver in Windows?  Do you build yourself
> against your own GDAL or against OSGeo4W?  (It's not in the CRAN
> windows-build).
>

I will check it later.

This is the error the CRAN build gives (though it's actually not
> recognizing the driver):
>
> "... does not exist in the file system, and is not recognised as a
> supported dataset name."
>

Exactly. And if I run traceback() after it, I find that it's the
'GDAL.open' function that is giving the error. In the error message I see
that the 'normalizePath' function is changing the variable name. For
example, if I use a file with a variable named "//DSSF", it gives:
"C:\Users\xxxx\AppData\Local\Temp\RtmpsD81tO\HDF5:201407291200:\DSSF"

Thanks

Oscar.

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Re: Problem reading a HDF5 file with readGDAL in Windows

Oscar Perpiñan-2
In reply to this post by Robert Hijmans
>
> Even better (renaming not necessary):
>
> x <-
> raster("E:/downloads/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5",
> var='Data Fields/ChiSquaredOfFit', ncdf=TRUE)
> >> Not a remedy, but the following might be a workable alternative...
> >>
> >>
> ncdf4::nc_open("OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5")$var$`Data
> >> Fields/ChiSquaredOfFit`
>

Thanks. It works with the file of the example. But it fails with this one
(even on a Linux machine):
https://www.dropbox.com/s/3zmhbtcpf7ly4nw/201407291200

> x <- raster('201407291200', var = 'DSSF', ncdf = TRUE)
Error in R_nc4_open: NetCDF: Can't open HDF5 attribute
....
> x <- raster('201407291200', var = '//DSSF', ncdf = TRUE)
Error in R_nc4_open: NetCDF: Can't open HDF5 attribute
....

However, I can open this file in Linux with:

x <- readGDAL('HDF5:201407291200://DSSF')

Best,

Oscar.

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Re: Problem reading a HDF5 file with readGDAL in Windows

Robert Hijmans
It works for me. I get:


> library(raster)
Loading required package: sp
> library(ncdf4)

> raster("E:/downloads/201407291200", ncdf=T, varname='DSSF')
class       : RasterLayer
dimensions  : 651, 1701, 1107351  (nrow, ncol, ncell)
resolution  : 1, 1  (x, y)
extent      : 0.5, 1701.5, 0.5, 651.5  (xmin, xmax, ymin, ymax)
coord. ref. : NA
data source : E:\downloads\201407291200
names       : DSSF
zvar        : DSSF


> sessionInfo()
R version 3.2.0 RC (2015-04-08 r68161)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United
States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ncdf4_1.12    raster_2.3-41 sp_1.0-17

loaded via a namespace (and not attached):
[1] grid_3.2.0      lattice_0.20-31
>


On Tue, May 5, 2015 at 10:53 PM, Oscar Perpiñan
<[hidden email]> wrote:

>> Even better (renaming not necessary):
>>
>> x <-
>> raster("E:/downloads/OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5",
>> var='Data Fields/ChiSquaredOfFit', ncdf=TRUE)
>> >> Not a remedy, but the following might be a workable alternative...
>> >>
>> >>
>> >> ncdf4::nc_open("OMI.L2.CloudOMCLDO2Strip200kmAlongCloudSat.2015.05.05.020752Z.v003.he5")$var$`Data
>> >> Fields/ChiSquaredOfFit`
>
>
> Thanks. It works with the file of the example. But it fails with this one
> (even on a Linux machine):
> https://www.dropbox.com/s/3zmhbtcpf7ly4nw/201407291200
>
>> x <- raster('201407291200', var = 'DSSF', ncdf = TRUE)
> Error in R_nc4_open: NetCDF: Can't open HDF5 attribute
> ....
>> x <- raster('201407291200', var = '//DSSF', ncdf = TRUE)
> Error in R_nc4_open: NetCDF: Can't open HDF5 attribute
> ....
>
> However, I can open this file in Linux with:
>
> x <- readGDAL('HDF5:201407291200://DSSF')
>
> Best,
>
> Oscar.

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Re: Problem reading a HDF5 file with readGDAL in Windows

Oscar Perpiñan-2
Not for me, and I cannot understand why:

> r <- raster("~/Dropbox/share/201407291200", ncdf=T, varname='DSSF')
Error in R_nc4_open: NetCDF: Can't open HDF5 attribute
Error in ncdf4::nc_open(filename) :
  Error in nc_open trying to open file
/home/oscar/Dropbox/share/201407291200
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: i586-pc-linux-gnu (32-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
 [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=es_ES.UTF-8
 [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=es_ES.UTF-8
 [7] LC_PAPER=es_ES.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ncdf4_1.13    raster_2.3-40 sp_1.0-14

loaded via a namespace (and not attached):
[1] compiler_3.2.0  tools_3.2.0     grid_3.2.0      lattice_0.20-27

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