Re: [netcdf-java] Linear algebra on data read from a netCDF file

• To: Konrad Hinsen <konrad.hinsen@xxxxxxxxxxxx>
• Subject: Re: [netcdf-java] Linear algebra on data read from a netCDF file
• From: John Caron <caron@xxxxxxxxxxxxxxxx>
• Date: Thu, 15 Oct 2009 09:51:23 -0600

Konrad Hinsen wrote:

I would like to do some data processing in Clojure (a JVM language), with the data being read from a netCDF file. The processing involves mostly standard linear algebra operations, e.g. singular value decomposition.

Both Colt and JAMA contain all the operations I need, but unfortunately they use different multiarray implementations than netCDF. I looks like I'd have to copy the data between two array classes, which is a pretty stupid (and inefficient) thing to do. Is there any other option? For example a linear algebra library that works directly on Unidata's Java array classes? If there is no other way than copying, what would be the most efficient approach?

Thanks,
  Konrad.

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Hi Konrad:

There are no known algebra packages using ucar.ma2.

The most efficient thing to use is this method on the Array class:

 public java.lang.Object get1DJavaArray(java.lang.Class wantType);

this will give back the java primitive array, without copying if possible. So 
if you have a double Array:

 double[] ja = (double []) ma.get1DJavaArray( double.class);

you then have to see if your chosen algebra package has a constructor that can 
wrap the java array without copying it. You will need the shape information:

 int[] shape = ma.getShape();

Good luck, and drop me a note if you find out anything useful to others with 
the same problem.

John

• Follow-Ups:
  • Re: [netcdf-java] Linear algebra on data read from a netCDF file
    • From: Konrad Hinsen
  • Re: [netcdf-java] Linear algebra on data read from a netCDF file
    • From: Doug Lindholm

• References:
  • [netcdf-java] Linear algebra on data read from a netCDF file
    • From: Konrad Hinsen