[R-sig-Geo] make a raster from Aquarius files

Fri Dec 1 21:57:03 CET 2017

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