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Re: [ferret_users] How proceed smi/hdf and bin/hdf (hdf4?) file to convert to hdf5 or netcdf in TDS?



Hi Dessy,
Ferret version 6.7 is linked with NetCDF 4, which uses the HDF library and can open hdf5 datasets.  I see on the oceancolor website that these are hdf4 files.
http://oceancolor.gsfc.nasa.gov/forum/oceancolor/topic_show.pl?tid=3246

So, our only option for reading these with Ferret is to put it onto a thredds server:  If you followed the directions to install a thredds server, then in your tomcat directory is a file, content/thredds/catalog.xml.  Edit that to add this dataset.  I downloaded the file T2012013001500.L2_LAC_OC, and so I added the following block of xml to the catalog.xml file to serve this dataset:   My catalog.xml starts like this, with the block I added in blue. You can use whatever names you like in dataset ID=, and name=. The location= is your local directory and file name.

<?xml version="1.0" encoding="UTF-8"?>
<catalog name="THREDDS Server Default Catalog : You must change this to fit your server!"
        xmlns="http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0"
        xmlns:xlink="http://www.w3.org/1999/xlink">

  <service name="all" base="" serviceType="compound">
    <service name="odap" serviceType="OpenDAP" base="/thredds/dodsC/" />
    <service name="http" serviceType="HTTPServer" base="/thredds/fileServer/" />
    <service name="wms" serviceType="WMS" base="/thredds/wms/"/>
  </service>

   <dataset ID="oceancolor" name="oceancolor file" urlPath="T2012013001500.L2_LAC_OC">
       <serviceName>all</serviceName>
       <netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2" location="/home/users/ansley/local/T2012013001500.L2_LAC_OC">
       </netcdf>
   </dataset>


...

Further datasets would each have a similar block of xml.

Then restart your thredds server, and then you'll be able to see the dataset in a browser. Use the address of your thredds server here, of course:

http://localhost:8080/thredds/dodsC/T2012013001500.L2_LAC_OC

Now you can open the file in Ferret:

yes? use "http://localhost:8080/thredds/dodsC/T2012013001500.L2_LAC_OC"
yes? show data





On 5/14/2012 1:48 AM, dessy berlianty wrote:
Dear Ferret-ers,

I have data which download from this website: http://oceancolor.gsfc.nasa.gov/cgi/l3 such as A20103212010328.L3m_8D_SST4_4.bz2 (SMI/HDF file) and A20101372010144.L3b_8D_SST4.main.bz2 (BIN/HDF file).
After extracted, I'd like to read in Ferret, but I have results as followings:

yes? use "/Downloads/A20103212010328.L3m_8D_SST4_4"
 **TMAP ERR: non-existent or not on line
             /Downloads/A20103212010328.L3m_8D_SST4_4(.des,.cdf,.nc)
yes? use "/Downloads/A20103212010328.L3m_8D_SST4_4.hdf"
 **TMAP ERR: non-existent or not on line
             /Downloads/A20103212010328.L3m_8D_SST4_4.hdf(.des,.cdf,.nc)
yes? show sym ferret*
FERRET_VERSION = "6.71"
FERRET_PLATFORM = "Linux 2.6.32-131.6.1.el6.x86_64 32-bit"
FERRET_MEMORY = "25.6"
yes? show sym net*
NETCDF_VERSION = "4.1.2 of Aug  3 2011 10:42:07 $"

Therefore, after I read mail archives here, then I install Java, Tomcat, and deploy TDS as in the instruction guidelines.
After I could access the http://localhost:8080/thredds/catalog.html, I'm loss my way to go to the next step how to upload my data to this server, and how to convert from SMI/HDF or BIN/HDF to HDF5 or netcdf.
Any suggestion would be really appreciated.
Thank you very much.

Best wishes,

dessy


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