Roy Mendelssohn wrote:
Hi Guys:
Are there any equivalent standalone tools that operate like ncdump and
ncgen but read/write NcML? What I am looking for is something easy
and scriptable that I can just go through our existing directories to
generate the NcML for each file, and then ultimately add some of the
georefencing info.
TIA,
-Roy M
Hi Roy:
This all pertains to the NetCDF-Java library:
You can generate NcML from a netcdf file by using NetcdfFile.writeNcML().
You can read NcML directly, just pass NetcdfFile.open() an NcML file
ending in .xml or .ncml.
You can write a NetcdfFile from a NcML file by opening it as above, then
using ucar.nc2.FileWriter.writeToFile().
You can do all all of this interactively by using the NcML Tab on the
ToolUI program at
http://www.unidata.ucar.edu/content/software/netcdf-java/v2.2/webstart/index.html
For your case, where I assume you want to add extra metadata, 2 paths
suggest itself:
1. Open the NetCDF file, add the extra metadata, then write it out
using FileWriter. (No NcML needed, do it all in Java) This might lend
itself to automatically doing a large amount of files.
2. Create the NcML file, add the extra metadata, then read it in and
write it back out using FileWriter to get a NetCDF file. For example I
have a file called example.nc, which has this NcML (whicj i generated
from ToolsUI):
<?xml version="1.0" encoding="UTF-8"?>
<netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2";
location="file:C:/dev/netcdf-java-2.2/test/data/dataset/example.nc">
<dimension name="time" length="4" isUnlimited="true" />
<dimension name="lat" length="3" />
<dimension name="lon" length="4" />
<attribute name="title" type="String" value="Example Data" />
<variable name="rh" shape="time lat lon" type="int">
<attribute name="long_name" type="String" value="relative humidity" />
<attribute name="units" type="String" value="percent" />
</variable>
<variable name="T" shape="time lat lon" type="double">
<attribute name="long_name" type="String" value="surface temperature" />
<attribute name="units" type="String" value="degC" />
</variable>
<variable name="lat" shape="lat" type="float">
<attribute name="units" type="String" value="degrees_north" />
</variable>
<variable name="lon" shape="lon" type="float">
<attribute name="units" type="String" value="degrees_east" />
</variable>
<variable name="time" shape="time" type="int">
<attribute name="units" type="String" value="hours" />
</variable>
</netcdf>
Now I add the "Conventions" global attribute :
<?xml version="1.0" encoding="UTF-8"?>
<netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2";
location="file:C:/dev/netcdf-java-2.2/test/data/dataset/example.nc">
<dimension name="time" length="4" isUnlimited="true" />
<dimension name="lat" length="3" />
<dimension name="lon" length="4" />
<attribute name="title" type="String" value="Example Data" />
<attribute name="Conventions" type="String" value="COARDS" />
<variable name="rh" shape="time lat lon" type="int">
<attribute name="long_name" type="String" value="relative humidity" />
<attribute name="units" type="String" value="percent" />
</variable>
<variable name="T" shape="time lat lon" type="double">
<attribute name="long_name" type="String" value="surface temperature" />
<attribute name="units" type="String" value="degC" />
</variable>
<variable name="lat" shape="lat" type="float">
<attribute name="units" type="String" value="degrees_north" />
</variable>
<variable name="lon" shape="lon" type="float">
<attribute name="units" type="String" value="degrees_east" />
</variable>
<variable name="time" shape="time" type="int">
<attribute name="units" type="String" value="hours" />
</variable>
</netcdf>
I actually dont need to add all information from the original file to
the NcML file, because the default is to read existing metadata in, so
equivilently:
<netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2";
location="file:C:/dev/netcdf-java-2.2/test/data/dataset/example.nc">
<attribute name="Conventions" type="String" value="COARDS" />
</netcdf>
If you need to add a new variable, just make sure you add its data
values also:
<netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2";
location="file:C:/dev/netcdf-java-2.2/test/data/dataset/example.nc">
<attribute name="Conventions" type="String" value="COARDS" />
<variable name="newvar" shape="time" type="float">
<values>1.0 4.5 7.8</values>
</variable>
</netcdf>
Once you have an NcML file, you can use FileWriter.main() in batch mode
to generate a NetCDF file:
> java -classpath toolsUI.jar ucar.nc2.FileWriter <ncml input
filename> <netcdf output filename>
