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

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  • Subject: Re: [netcdf-java] Linear algebra on data read from a netCDF file (fwd)
  • Date: Sun, 18 Oct 2009 09:25:09 -0600 (MDT)


===============================================================================
Robb Kambic                                Unidata Program Center
Software Engineer III                      Univ. Corp for Atmospheric Research
address@hidden             WWW: http://www.unidata.ucar.edu/
===============================================================================

---------- Forwarded message ----------
Date: Sun, 18 Oct 2009 13:13:12 +0200
From: Konrad Hinsen <address@hidden>
To: address@hidden
Subject: Re: [netcdf-java] Linear algebra on data read from a netCDF file

On 16 Oct 2009, at 14:06, Konrad Hinsen wrote:
Thanks! This should at least be efficient. I quickly checked the Colt implementation, which does have a constructor for its array class that takes the plain Java array plus the shape information, so at least in theory this should be simple. If/when I get it to work, I'll post my solution here.
Here is a working example (Clojure source code) for inverting a matrix read from a netCDF file using Colt: 

(ns netcdf-read
 (:import (ucar.nc2 NetcdfFile)
           (cern.colt.matrix.tdouble.impl DenseDoubleMatrix2D)
           (cern.colt.matrix.tdouble.algo DenseDoubleAlgebra)))

(defn unidata-to-colt
 [#^ucar.ma2.ArrayDouble$D2 array]
 (let [java-array-1d (.get1DJavaArray array Double)
        [rows, cols]  (.getShape array)]
   (new DenseDoubleMatrix2D rows cols java-array-1d 0 0 cols 1 false)))
(let [matrix (with-open [ncfile (NetcdfFile/open "/Users/hinsen/Temp/matrix.nc")] 
                    (.read (.findVariable ncfile "matrix")))
     colt-matrix (unidata-to-colt matrix)
     la          (new DenseDoubleAlgebra)
     inverse     (.inverse la colt-matrix)]
 (prn inverse))
For my current needs, conversion of 2D double arrays is sufficient, but this could of course be generalized to ranks 1 and 3 (that's all there is in Colt) and other element types. 

Konrad.

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