make a raster from Aquarius files

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make a raster from Aquarius files

Antonio Silva
Hello

Some time ago I prepared scripts to extract temperature data from Modis
Aqua files. It can be found at https://gist.github.com/aolinto

HDF files can be downloaded at https://oceancolor.gsfc.nasa.gov/cgi/l3

I got the Aquarius sea surface salinity smoothed file from June 2015.

I could open and read the file:

library(ncdf4)
library(raster)

nc.data<-nc_open("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg")
print(nc.data)
dim(ncvar_get(nc.data,"l3m_data"))
ncvar_get(nc.data,"l3m_data")[c(110:160),c(110:117)]

But I could not prepare a raster from it. I tryed many things as:

rst.data <-
raster("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg",varname="l3m_data")
Error in .local(.Object, ...) :
  `AQUARIUS/Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg' not recognised as a
supported file format.

Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",
:
  Cannot create a RasterLayer object from this file.

and variations with band and layer.

I would greatly appreciate any suggestions to solve this issue.

Thanks

--
Antônio Olinto Ávila da Silva
Fisheries Institute
São Paulo, Brasil

        [[alternative HTML version deleted]]

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Re: make a raster from Aquarius files

Michael Sumner-2
That file name does not correspond to the standard patterns used by the
oceancolor site. All the L3m products from there are now (NetCDF 4.0) .nc
and so will work fine with raster/ncdf4.  (Some years ago they were HDF4 -
without an extension, as the shortcuts in the image thumbnails hints
(SMI/HDF and BIN/HDF - SMI/L3m standard mapped image in your case).

I think you've got some other provider's version of a file, but there's not
enough information here to know where you got it or what form it's in. I'm
happy to look if you can point us to the source of
Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.

But otherwise, can you share with us the output of

nc.data<-nc_open("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg")
print(nc.data)

and if you're on a suitable system with HDF4 support a gdalinfo output of
the file would be useful too.

Given that you can read it with ncdf4, and if it actually is NetCDF4 (not
HDF4 or something else) you might help raster work with it by renaming it
to "Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.nc" since (unlike GDAL and
the NetCDF lib itself) raster uses explicit extension to dispatch to
different format logic code, though it ultimately sends it down to rgdal to
deal with if it can't recognize it - which is why I'm surprised you can't
get it to work and ( I'm guessing wildly now):

Do you not have rgdal installed?


What system are you on? Please use sessionInfo() to share details.

Cheers, Mike.
On Fri, 1 Dec 2017, 06:14 Antonio Silva, <[hidden email]> wrote:

> Hello
>
> Some time ago I prepared scripts to extract temperature data from Modis
> Aqua files. It can be found at https://gist.github.com/aolinto
>
> HDF files can be downloaded at https://oceancolor.gsfc.nasa.gov/cgi/l3
>
> I got the Aquarius sea surface salinity smoothed file from June 2015.
>
> I could open and read the file:
>
> library(ncdf4)
> library(raster)
>
> nc.data<-nc_open("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg")
> print(nc.data)
> dim(ncvar_get(nc.data,"l3m_data"))
> ncvar_get(nc.data,"l3m_data")[c(110:160),c(110:117)]
>
> But I could not prepare a raster from it. I tryed many things as:
>
> rst.data <-
> raster("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg",varname="l3m_data")
> Error in .local(.Object, ...) :
>   `AQUARIUS/Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg' not recognised as a
> supported file format.
>
> Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",
> :
>   Cannot create a RasterLayer object from this file.
>
> and variations with band and layer.
>
> I would greatly appreciate any suggestions to solve this issue.
>
> Thanks
>
> --
> Antônio Olinto Ávila da Silva
> Fisheries Institute
> São Paulo, Brasil
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo

--
Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia

        [[alternative HTML version deleted]]

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Re: make a raster from Aquarius files

Ben Tupper
Hi,

Those Aquarius files look quite different from others I have used from OBPG (mostly MODISA and SeaWiFS).

As a short-cut alternative, you could read all of the values into a matrix and make a global raster from that.  An example is shown below.  You can also subset the extraction as you have shown, but it might be easier to subset after making the raster using raster::crop()

CHeers,
Ben


### START

library(raster)
library(ncdf4)
library(rasterVis)

filename = "Q20151522015181.L3m_MO_SCIA_V5.0_SSS_1deg"

nc = ncdf4::nc_open(filename)
m = ncdf4::ncvar_get(nc, 'l3m_data')
ncdf4::nc_close(nc)
r = raster::raster(t(m))
rasterVis::levelplot(r)

### END

> On Dec 1, 2017, at 6:24 AM, Michael Sumner <[hidden email]> wrote:
>
> That file name does not correspond to the standard patterns used by the
> oceancolor site. All the L3m products from there are now (NetCDF 4.0) .nc
> and so will work fine with raster/ncdf4.  (Some years ago they were HDF4 -
> without an extension, as the shortcuts in the image thumbnails hints
> (SMI/HDF and BIN/HDF - SMI/L3m standard mapped image in your case).
>
> I think you've got some other provider's version of a file, but there's not
> enough information here to know where you got it or what form it's in. I'm
> happy to look if you can point us to the source of
> Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.
>
> But otherwise, can you share with us the output of
>
> nc.data<-nc_open("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg")
> print(nc.data)
>
> and if you're on a suitable system with HDF4 support a gdalinfo output of
> the file would be useful too.
>
> Given that you can read it with ncdf4, and if it actually is NetCDF4 (not
> HDF4 or something else) you might help raster work with it by renaming it
> to "Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.nc" since (unlike GDAL and
> the NetCDF lib itself) raster uses explicit extension to dispatch to
> different format logic code, though it ultimately sends it down to rgdal to
> deal with if it can't recognize it - which is why I'm surprised you can't
> get it to work and ( I'm guessing wildly now):
>
> Do you not have rgdal installed?
>
>
> What system are you on? Please use sessionInfo() to share details.
>
> Cheers, Mike.
> On Fri, 1 Dec 2017, 06:14 Antonio Silva, <[hidden email]> wrote:
>
>> Hello
>>
>> Some time ago I prepared scripts to extract temperature data from Modis
>> Aqua files. It can be found at https://gist.github.com/aolinto
>>
>> HDF files can be downloaded at https://oceancolor.gsfc.nasa.gov/cgi/l3
>>
>> I got the Aquarius sea surface salinity smoothed file from June 2015.
>>
>> I could open and read the file:
>>
>> library(ncdf4)
>> library(raster)
>>
>> nc.data<-nc_open("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg")
>> print(nc.data)
>> dim(ncvar_get(nc.data,"l3m_data"))
>> ncvar_get(nc.data,"l3m_data")[c(110:160),c(110:117)]
>>
>> But I could not prepare a raster from it. I tryed many things as:
>>
>> rst.data <-
>> raster("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg",varname="l3m_data")
>> Error in .local(.Object, ...) :
>>  `AQUARIUS/Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg' not recognised as a
>> supported file format.
>>
>> Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",
>> :
>>  Cannot create a RasterLayer object from this file.
>>
>> and variations with band and layer.
>>
>> I would greatly appreciate any suggestions to solve this issue.
>>
>> Thanks
>>
>> --
>> Antônio Olinto Ávila da Silva
>> Fisheries Institute
>> São Paulo, Brasil
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
> --
> Dr. Michael Sumner
> Software and Database Engineer
> Australian Antarctic Division
> 203 Channel Highway
> Kingston Tasmania 7050 Australia
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo

Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org

Ecocast Reports: http://seascapemodeling.org/ecocast.html
Tick Reports: https://report.bigelow.org/tick/
Jellyfish Reports: https://jellyfish.bigelow.org/jellyfish/

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Re: make a raster from Aquarius files

Antonio Silva
Thanks Ben and Michael for the attention

The file I'm trying to rasterize can be downloaded at
https://oceancolor.gsfc.nasa.gov/cgi/l3

I selected the Aquarius sea surface salinity smoothed file from June 2015
(SMI HDF).

As Ben pointed it is also available from OBPG Nasa Ocean Color site at
https://oceandata.sci.gsfc.nasa.gov/Aquarius/Mapped/Monthly/1deg/V5.0_SSS/

or directly from
https://oceandata.sci.gsfc.nasa.gov/cgi/getfile/Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.bz2

Thanks again

Antonio Olinto Avila da Silva
Fisheries Institute
São Paulo, Brasil


2017-12-01 12:35 GMT-02:00 Ben Tupper <[hidden email]>:

> Hi,
>
> Those Aquarius files look quite different from others I have used from
> OBPG (mostly MODISA and SeaWiFS).
>
> As a short-cut alternative, you could read all of the values into a matrix
> and make a global raster from that.  An example is shown below.  You can
> also subset the extraction as you have shown, but it might be easier to
> subset after making the raster using raster::crop()
>
> CHeers,
> Ben
>
>
> ### START
>
> library(raster)
> library(ncdf4)
> library(rasterVis)
>
> filename = "Q20151522015181.L3m_MO_SCIA_V5.0_SSS_1deg"
>
> nc = ncdf4::nc_open(filename)
> m = ncdf4::ncvar_get(nc, 'l3m_data')
> ncdf4::nc_close(nc)
> r = raster::raster(t(m))
> rasterVis::levelplot(r)
>
> ### END
>
> > On Dec 1, 2017, at 6:24 AM, Michael Sumner <[hidden email]> wrote:
> >
> > That file name does not correspond to the standard patterns used by the
> > oceancolor site. All the L3m products from there are now (NetCDF 4.0) .nc
> > and so will work fine with raster/ncdf4.  (Some years ago they were HDF4
> -
> > without an extension, as the shortcuts in the image thumbnails hints
> > (SMI/HDF and BIN/HDF - SMI/L3m standard mapped image in your case).
> >
> > I think you've got some other provider's version of a file, but there's
> not
> > enough information here to know where you got it or what form it's in.
> I'm
> > happy to look if you can point us to the source of
> > Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.
> >
> > But otherwise, can you share with us the output of
> >
> > nc.data<-nc_open("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg")
> > print(nc.data)
> >
> > and if you're on a suitable system with HDF4 support a gdalinfo output of
> > the file would be useful too.
> >
> > Given that you can read it with ncdf4, and if it actually is NetCDF4 (not
> > HDF4 or something else) you might help raster work with it by renaming it
> > to "Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.nc" since (unlike GDAL
> and
> > the NetCDF lib itself) raster uses explicit extension to dispatch to
> > different format logic code, though it ultimately sends it down to rgdal
> to
> > deal with if it can't recognize it - which is why I'm surprised you can't
> > get it to work and ( I'm guessing wildly now):
> >
> > Do you not have rgdal installed?
> >
> >
> > What system are you on? Please use sessionInfo() to share details.
> >
> > Cheers, Mike.
> > On Fri, 1 Dec 2017, 06:14 Antonio Silva, <[hidden email]> wrote:
> >
> >> Hello
> >>
> >> Some time ago I prepared scripts to extract temperature data from Modis
> >> Aqua files. It can be found at https://gist.github.com/aolinto
> >>
> >> HDF files can be downloaded at https://oceancolor.gsfc.nasa.gov/cgi/l3
> >>
> >> I got the Aquarius sea surface salinity smoothed file from June 2015.
> >>
> >> I could open and read the file:
> >>
> >> library(ncdf4)
> >> library(raster)
> >>
> >> nc.data<-nc_open("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg")
> >> print(nc.data)
> >> dim(ncvar_get(nc.data,"l3m_data"))
> >> ncvar_get(nc.data,"l3m_data")[c(110:160),c(110:117)]
> >>
> >> But I could not prepare a raster from it. I tryed many things as:
> >>
> >> rst.data <-
> >> raster("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg",varname="l3m_data")
> >> Error in .local(.Object, ...) :
> >>  `AQUARIUS/Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg' not recognised
> as a
> >> supported file format.
> >>
> >> Error in .rasterObjectFromFile(x, band = band, objecttype =
> "RasterLayer",
> >> :
> >>  Cannot create a RasterLayer object from this file.
> >>
> >> and variations with band and layer.
> >>
> >> I would greatly appreciate any suggestions to solve this issue.
> >>
> >> Thanks
> >>
> >> --
> >> Antônio Olinto Ávila da Silva
> >> Fisheries Institute
> >> São Paulo, Brasil
> >>
> >>        [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> R-sig-Geo mailing list
> >> [hidden email]
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
> > --
> > Dr. Michael Sumner
> > Software and Database Engineer
> > Australian Antarctic Division
> > 203 Channel Highway
> > Kingston Tasmania 7050 Australia
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > [hidden email]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org
>
> Ecocast Reports: http://seascapemodeling.org/ecocast.html
> Tick Reports: https://report.bigelow.org/tick/
> Jellyfish Reports: https://jellyfish.bigelow.org/jellyfish/
>
>
>
>

        [[alternative HTML version deleted]]

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Re: make a raster from Aquarius files

Michael Sumner-2
Ah thanks, and sorry I didn't think any of those old HDF4 files were still
there!

This is HDF5 with subdatasets, from gdalinfo:

Subdatasets:

SUBDATASET_1_NAME=HDF5:"Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg"://l3m_data
  SUBDATASET_1_DESC=[180x360] //l3m_data (32-bit floating-point)

SUBDATASET_2_NAME=HDF5:"Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg"://palette
  SUBDATASET_2_DESC=[3x256] //palette (8-bit unsigned character)

so you need to use the subdataset string directly i.e.

raster("HDF5:"Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg")

or spit them out to seperate files at the command line first e.g.

gdal_translate Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg
Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.tif -sds

and this assumes a suitable system with HDF5 etc. etc.

rgdal on Windows now has HDF5 drivers so should work there too, and Ben's
method also.

Cheers, Mike.

On Sat, 2 Dec 2017 at 07:27 Antonio Silva <[hidden email]> wrote:

> Thanks Ben and Michael for the attention
>
> The file I'm trying to rasterize can be downloaded at
> https://oceancolor.gsfc.nasa.gov/cgi/l3
>
> I selected the Aquarius sea surface salinity smoothed file from June 2015
> (SMI HDF).
>
> As Ben pointed it is also available from OBPG Nasa Ocean Color site at
> https://oceandata.sci.gsfc.nasa.gov/Aquarius/Mapped/Monthly/1deg/V5.0_SSS/
>
> or directly from
> https://oceandata.sci.gsfc.nasa.gov/cgi/getfile/Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.bz2
>
> Thanks again
>
> Antonio Olinto Avila da Silva
> Fisheries Institute
> São Paulo, Brasil
>
>
> 2017-12-01 12:35 GMT-02:00 Ben Tupper <[hidden email]>:
>
>> Hi,
>>
>> Those Aquarius files look quite different from others I have used from
>> OBPG (mostly MODISA and SeaWiFS).
>>
>> As a short-cut alternative, you could read all of the values into a
>> matrix and make a global raster from that.  An example is shown below.  You
>> can also subset the extraction as you have shown, but it might be easier to
>> subset after making the raster using raster::crop()
>>
>> CHeers,
>> Ben
>>
>>
>> ### START
>>
>> library(raster)
>> library(ncdf4)
>> library(rasterVis)
>>
>> filename = "Q20151522015181.L3m_MO_SCIA_V5.0_SSS_1deg"
>>
>> nc = ncdf4::nc_open(filename)
>> m = ncdf4::ncvar_get(nc, 'l3m_data')
>> ncdf4::nc_close(nc)
>> r = raster::raster(t(m))
>> rasterVis::levelplot(r)
>>
>> ### END
>>
>> > On Dec 1, 2017, at 6:24 AM, Michael Sumner <[hidden email]> wrote:
>> >
>> > That file name does not correspond to the standard patterns used by the
>> > oceancolor site. All the L3m products from there are now (NetCDF 4.0)
>> .nc
>> > and so will work fine with raster/ncdf4.  (Some years ago they were
>> HDF4 -
>> > without an extension, as the shortcuts in the image thumbnails hints
>> > (SMI/HDF and BIN/HDF - SMI/L3m standard mapped image in your case).
>> >
>> > I think you've got some other provider's version of a file, but there's
>> not
>> > enough information here to know where you got it or what form it's in.
>> I'm
>> > happy to look if you can point us to the source of
>> > Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.
>> >
>> > But otherwise, can you share with us the output of
>> >
>> > nc.data<-nc_open("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg")
>> > print(nc.data)
>> >
>> > and if you're on a suitable system with HDF4 support a gdalinfo output
>> of
>> > the file would be useful too.
>> >
>> > Given that you can read it with ncdf4, and if it actually is NetCDF4
>> (not
>> > HDF4 or something else) you might help raster work with it by renaming
>> it
>> > to "Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.nc" since (unlike GDAL
>> and
>> > the NetCDF lib itself) raster uses explicit extension to dispatch to
>> > different format logic code, though it ultimately sends it down to
>> rgdal to
>> > deal with if it can't recognize it - which is why I'm surprised you
>> can't
>> > get it to work and ( I'm guessing wildly now):
>> >
>> > Do you not have rgdal installed?
>> >
>> >
>> > What system are you on? Please use sessionInfo() to share details.
>> >
>> > Cheers, Mike.
>> > On Fri, 1 Dec 2017, 06:14 Antonio Silva, <[hidden email]> wrote:
>> >
>> >> Hello
>> >>
>> >> Some time ago I prepared scripts to extract temperature data from Modis
>> >> Aqua files. It can be found at https://gist.github.com/aolinto
>> >>
>> >> HDF files can be downloaded at https://oceancolor.gsfc.nasa.gov/cgi/l3
>> >>
>> >> I got the Aquarius sea surface salinity smoothed file from June 2015.
>> >>
>> >> I could open and read the file:
>> >>
>> >> library(ncdf4)
>> >> library(raster)
>> >>
>> >> nc.data<-nc_open("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg")
>> >> print(nc.data)
>> >> dim(ncvar_get(nc.data,"l3m_data"))
>> >> ncvar_get(nc.data,"l3m_data")[c(110:160),c(110:117)]
>> >>
>> >> But I could not prepare a raster from it. I tryed many things as:
>> >>
>> >> rst.data <-
>> >> raster("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg",varname="l3m_data")
>> >> Error in .local(.Object, ...) :
>> >>  `AQUARIUS/Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg' not recognised
>> as a
>> >> supported file format.
>> >>
>> >> Error in .rasterObjectFromFile(x, band = band, objecttype =
>> "RasterLayer",
>> >> :
>> >>  Cannot create a RasterLayer object from this file.
>> >>
>> >> and variations with band and layer.
>> >>
>> >> I would greatly appreciate any suggestions to solve this issue.
>> >>
>> >> Thanks
>> >>
>> >> --
>> >> Antônio Olinto Ávila da Silva
>> >> Fisheries Institute
>> >> São Paulo, Brasil
>> >>
>> >>        [[alternative HTML version deleted]]
>> >>
>> >> _______________________________________________
>> >> R-sig-Geo mailing list
>> >> [hidden email]
>> >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>> >
>> > --
>> > Dr. Michael Sumner
>> > Software and Database Engineer
>> > Australian Antarctic Division
>> > 203 Channel Highway
>> <https://maps.google.com/?q=203+Channel+Highway+%0D+%3E+Kingston+Tasmania+7050+Australia&entry=gmail&source=g>
>>
>> <https://maps.google.com/?q=203+Channel+Highway+%0D+%3E+Kingston+Tasmania+7050+Australia&entry=gmail&source=g>>
>> Kingston Tasmania 7050 Australia
>> <https://maps.google.com/?q=203+Channel+Highway+%0D+%3E+Kingston+Tasmania+7050+Australia&entry=gmail&source=g>
>> >
>> >       [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > R-sig-Geo mailing list
>> > [hidden email]
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>> Ben Tupper
>> Bigelow Laboratory for Ocean Sciences
>> 60 Bigelow Drive
>> <https://maps.google.com/?q=60+Bigelow+Drive&entry=gmail&source=g>, P.O.
>> Box 380
>> East Boothbay, Maine 04544
>> http://www.bigelow.org
>>
>> Ecocast Reports: http://seascapemodeling.org/ecocast.html
>> Tick Reports: https://report.bigelow.org/tick/
>> Jellyfish Reports: https://jellyfish.bigelow.org/jellyfish/
>>
>>
>>
>>
>
>
>
> --
Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia

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Re: make a raster from Aquarius files

Michael Sumner-2
Ugh, and you must think I'm crazy given that it's clearly HDF5 not HDF4 as
per my opening line (the file naming is more the latter). I'll stop now.
Hope it's useful.

Cheers, Mike.

On Sat, 2 Dec 2017 at 07:44 Michael Sumner <[hidden email]> wrote:

> Ah thanks, and sorry I didn't think any of those old HDF4 files were still
> there!
>
> This is HDF5 with subdatasets, from gdalinfo:
>
> Subdatasets:
>
> SUBDATASET_1_NAME=HDF5:"Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg"://l3m_data
>   SUBDATASET_1_DESC=[180x360] //l3m_data (32-bit floating-point)
>
> SUBDATASET_2_NAME=HDF5:"Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg"://palette
>   SUBDATASET_2_DESC=[3x256] //palette (8-bit unsigned character)
>
> so you need to use the subdataset string directly i.e.
>
> raster("HDF5:"Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg")
>
> or spit them out to seperate files at the command line first e.g.
>
> gdal_translate Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg
> Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.tif -sds
>
> and this assumes a suitable system with HDF5 etc. etc.
>
> rgdal on Windows now has HDF5 drivers so should work there too, and Ben's
> method also.
>
> Cheers, Mike.
>
> On Sat, 2 Dec 2017 at 07:27 Antonio Silva <[hidden email]> wrote:
>
>> Thanks Ben and Michael for the attention
>>
>> The file I'm trying to rasterize can be downloaded at
>> https://oceancolor.gsfc.nasa.gov/cgi/l3
>>
>> I selected the Aquarius sea surface salinity smoothed file from June 2015
>> (SMI HDF).
>>
>> As Ben pointed it is also available from OBPG Nasa Ocean Color site at
>> https://oceandata.sci.gsfc.nasa.gov/Aquarius/Mapped/Monthly/1deg/V5.0_SSS/
>>
>> or directly from
>> https://oceandata.sci.gsfc.nasa.gov/cgi/getfile/Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.bz2
>>
>> Thanks again
>>
>> Antonio Olinto Avila da Silva
>> Fisheries Institute
>> São Paulo, Brasil
>>
>>
>> 2017-12-01 12:35 GMT-02:00 Ben Tupper <[hidden email]>:
>>
>>> Hi,
>>>
>>> Those Aquarius files look quite different from others I have used from
>>> OBPG (mostly MODISA and SeaWiFS).
>>>
>>> As a short-cut alternative, you could read all of the values into a
>>> matrix and make a global raster from that.  An example is shown below.  You
>>> can also subset the extraction as you have shown, but it might be easier to
>>> subset after making the raster using raster::crop()
>>>
>>> CHeers,
>>> Ben
>>>
>>>
>>> ### START
>>>
>>> library(raster)
>>> library(ncdf4)
>>> library(rasterVis)
>>>
>>> filename = "Q20151522015181.L3m_MO_SCIA_V5.0_SSS_1deg"
>>>
>>> nc = ncdf4::nc_open(filename)
>>> m = ncdf4::ncvar_get(nc, 'l3m_data')
>>> ncdf4::nc_close(nc)
>>> r = raster::raster(t(m))
>>> rasterVis::levelplot(r)
>>>
>>> ### END
>>>
>>> > On Dec 1, 2017, at 6:24 AM, Michael Sumner <[hidden email]> wrote:
>>> >
>>> > That file name does not correspond to the standard patterns used by the
>>> > oceancolor site. All the L3m products from there are now (NetCDF 4.0)
>>> .nc
>>> > and so will work fine with raster/ncdf4.  (Some years ago they were
>>> HDF4 -
>>> > without an extension, as the shortcuts in the image thumbnails hints
>>> > (SMI/HDF and BIN/HDF - SMI/L3m standard mapped image in your case).
>>> >
>>> > I think you've got some other provider's version of a file, but
>>> there's not
>>> > enough information here to know where you got it or what form it's in.
>>> I'm
>>> > happy to look if you can point us to the source of
>>> > Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.
>>> >
>>> > But otherwise, can you share with us the output of
>>> >
>>> > nc.data<-nc_open("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg")
>>> > print(nc.data)
>>> >
>>> > and if you're on a suitable system with HDF4 support a gdalinfo output
>>> of
>>> > the file would be useful too.
>>> >
>>> > Given that you can read it with ncdf4, and if it actually is NetCDF4
>>> (not
>>> > HDF4 or something else) you might help raster work with it by renaming
>>> it
>>> > to "Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg.nc" since (unlike GDAL
>>> and
>>> > the NetCDF lib itself) raster uses explicit extension to dispatch to
>>> > different format logic code, though it ultimately sends it down to
>>> rgdal to
>>> > deal with if it can't recognize it - which is why I'm surprised you
>>> can't
>>> > get it to work and ( I'm guessing wildly now):
>>> >
>>> > Do you not have rgdal installed?
>>> >
>>> >
>>> > What system are you on? Please use sessionInfo() to share details.
>>> >
>>> > Cheers, Mike.
>>> > On Fri, 1 Dec 2017, 06:14 Antonio Silva, <[hidden email]>
>>> wrote:
>>> >
>>> >> Hello
>>> >>
>>> >> Some time ago I prepared scripts to extract temperature data from
>>> Modis
>>> >> Aqua files. It can be found at https://gist.github.com/aolinto
>>> >>
>>> >> HDF files can be downloaded at
>>> https://oceancolor.gsfc.nasa.gov/cgi/l3
>>> >>
>>> >> I got the Aquarius sea surface salinity smoothed file from June 2015.
>>> >>
>>> >> I could open and read the file:
>>> >>
>>> >> library(ncdf4)
>>> >> library(raster)
>>> >>
>>> >> nc.data<-nc_open("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg")
>>> >> print(nc.data)
>>> >> dim(ncvar_get(nc.data,"l3m_data"))
>>> >> ncvar_get(nc.data,"l3m_data")[c(110:160),c(110:117)]
>>> >>
>>> >> But I could not prepare a raster from it. I tryed many things as:
>>> >>
>>> >> rst.data <-
>>> >>
>>> raster("Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg",varname="l3m_data")
>>> >> Error in .local(.Object, ...) :
>>> >>  `AQUARIUS/Q20151522015181.L3m_MO_SCISM_V5.0_SSS_1deg' not recognised
>>> as a
>>> >> supported file format.
>>> >>
>>> >> Error in .rasterObjectFromFile(x, band = band, objecttype =
>>> "RasterLayer",
>>> >> :
>>> >>  Cannot create a RasterLayer object from this file.
>>> >>
>>> >> and variations with band and layer.
>>> >>
>>> >> I would greatly appreciate any suggestions to solve this issue.
>>> >>
>>> >> Thanks
>>> >>
>>> >> --
>>> >> Antônio Olinto Ávila da Silva
>>> >> Fisheries Institute
>>> >> São Paulo, Brasil
>>> >>
>>> >>        [[alternative HTML version deleted]]
>>> >>
>>> >> _______________________________________________
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>>> >
>>> > --
>>> > Dr. Michael Sumner
>>> > Software and Database Engineer
>>> > Australian Antarctic Division
>>> > 203 Channel Highway
>>> <https://maps.google.com/?q=203+Channel+Highway+%0D+%3E+Kingston+Tasmania+7050+Australia&entry=gmail&source=g>
>>>
>>> <https://maps.google.com/?q=203+Channel+Highway+%0D+%3E+Kingston+Tasmania+7050+Australia&entry=gmail&source=g>>
>>> Kingston Tasmania 7050 Australia
>>> <https://maps.google.com/?q=203+Channel+Highway+%0D+%3E+Kingston+Tasmania+7050+Australia&entry=gmail&source=g>
>>> >
>>> >       [[alternative HTML version deleted]]
>>> >
>>> > _______________________________________________
>>> > R-sig-Geo mailing list
>>> > [hidden email]
>>> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>> Ben Tupper
>>> Bigelow Laboratory for Ocean Sciences
>>> 60 Bigelow Drive
>>> <https://maps.google.com/?q=60+Bigelow+Drive&entry=gmail&source=g>,
>>> P.O. Box 380
>>> East Boothbay, Maine 04544
>>> http://www.bigelow.org
>>>
>>> Ecocast Reports: http://seascapemodeling.org/ecocast.html
>>> Tick Reports: https://report.bigelow.org/tick/
>>> Jellyfish Reports: https://jellyfish.bigelow.org/jellyfish/
>>>
>>>
>>>
>>>
>>
>>
>>
>> --
> Dr. Michael Sumner
> Software and Database Engineer
> Australian Antarctic Division
> 203 Channel Highway
> Kingston Tasmania 7050 Australia
>
> --
Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia

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