[R-sig-Geo] 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 <btupper at bigelow.org>:

> 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 <mdsumner at gmail.com> 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, <aolinto.lst at gmail.com> 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
> >> R-sig-Geo at r-project.org
> >> 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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> > 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
>
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