[Jigs-commits] CVS: jigs/src/edu/whitman/halfway/util ProcessUtil.java, 1.5, 1.6 MathUtil.java, 1.3, 1.4 MiscUtil.java, 1.24, 1.25 PropProvider.java, 1.5, 1.6 EADoubleFactory2D.java, 1.2, 1.3

[Brendan M. <mc...@us...>]

Update of /cvsroot/jigs/jigs/src/edu/whitman/halfway/util
In directory sc8-pr-cvs6.sourceforge.net:/tmp/cvs-serv20896/src/edu/whitman/halfway/util

Modified Files:
	ProcessUtil.java MathUtil.java MiscUtil.java PropProvider.java 
	EADoubleFactory2D.java 
Log Message:


Index: ProcessUtil.java
===================================================================
RCS file: /cvsroot/jigs/jigs/src/edu/whitman/halfway/util/ProcessUtil.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** ProcessUtil.java	16 May 2005 22:59:47 -0000	1.5
--- ProcessUtil.java	11 Nov 2006 02:04:56 -0000	1.6
***************
*** 13,16 ****
--- 13,20 ----
      
      private static Logger log = Logger.getLogger(ProcessUtil.class.getName());
+     
+     public static boolean exec(String[] command, OutputStream out){
+         return exec(command, out, null);
+     }
  
      /** Tries to exec the command, waits for it to finsih, logs errors if
***************
*** 19,27 ****
          becomes available ... pass in System.out to monitor
          progress.*/
!     public static boolean exec(String[] command, OutputStream out){
          Process proc;
          try{
              log.debug("Trying to execute command " + Arrays.asList(command));
!             proc = Runtime.getRuntime().exec(command);
          }catch(IOException e){
              log.error("IOException while trying to execute " + command, e);
--- 23,31 ----
          becomes available ... pass in System.out to monitor
          progress.*/
!     public static boolean exec(String[] command, OutputStream out, File workingDir){
          Process proc;
          try{
              log.debug("Trying to execute command " + Arrays.asList(command));
!             proc = Runtime.getRuntime().exec(command, null, workingDir);
          }catch(IOException e){
              log.error("IOException while trying to execute " + command, e);

Index: MathUtil.java
===================================================================
RCS file: /cvsroot/jigs/jigs/src/edu/whitman/halfway/util/MathUtil.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** MathUtil.java	20 Mar 2004 00:07:23 -0000	1.3
--- MathUtil.java	11 Nov 2006 02:04:56 -0000	1.4
***************
*** 23,26 ****
--- 23,30 ----
      public static final double TWO_PI = Math.PI * 2;
  
+     
+     
+     
+     
      /** Given the function f and the step-paramter t, returns
       * extimates of the gradients */

Index: MiscUtil.java
===================================================================
RCS file: /cvsroot/jigs/jigs/src/edu/whitman/halfway/util/MiscUtil.java,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** MiscUtil.java	11 Sep 2006 15:05:22 -0000	1.24
--- MiscUtil.java	11 Nov 2006 02:04:56 -0000	1.25
***************
*** 7,1175 ****
  import java.util.*;
  
! public final class MiscUtil{
!     
!     private static Logger log = Logger.getLogger(MiscUtil.class);
  
!     //private static DecimalFormat df = new DecimalFormat("0.000E0");
!     private static DecimalFormat df = new DecimalFormat("0.000");
  
!     private static Random rand = new Random();
[...2445 lines suppressed...]
+     }
+     System.out.println("Sorting Results (key array over value array): ");
+     MiscUtil.simpleSortDecPairs(key, value);
+     System.out.println(MiscUtil.toString(key));
+     System.out.print(MiscUtil.toString(value));
+     System.out.println();
  
!     System.out.println("Testing unpack methods on 1, ..., 9");
!     double[] d = { 1, 2, 3, 4, 5, 6, 7, 8, 9 };
!     System.out.println("Unpack Row Major:");
!     double[][] rm = unpackRowMajor(3, 3, d);
!     System.out.println(MiscUtil.toString(rm));
!     System.out.println(MiscUtil.toString(MiscUtil.packRowMajor(rm)));
  
!     System.out.println("Column Major:");
!     double[][] cm = unpackColMajor(3, 3, d);
!     System.out.println(MiscUtil.toString(cm));
!   }
  
  }

Index: PropProvider.java
===================================================================
RCS file: /cvsroot/jigs/jigs/src/edu/whitman/halfway/util/PropProvider.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** PropProvider.java	11 Sep 2006 15:05:22 -0000	1.5
--- PropProvider.java	11 Nov 2006 02:04:56 -0000	1.6
***************
*** 38,43 ****
                  }
              }else{
!                 log.info("Skipping field " + fields[i].getName());
                  log.debug("Skipped because of modifiers: " + Modifier.toString(mods));
              }
          }
--- 38,45 ----
                  }
              }else{
!               if(log.isDebugEnabled()){
!                 log.debug("Skipping field " + fields[i].getName());
                  log.debug("Skipped because of modifiers: " + Modifier.toString(mods));
+               }
              }
          }

Index: EADoubleFactory2D.java
===================================================================
RCS file: /cvsroot/jigs/jigs/src/edu/whitman/halfway/util/EADoubleFactory2D.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** EADoubleFactory2D.java	12 Jan 2004 20:06:43 -0000	1.2
--- EADoubleFactory2D.java	11 Nov 2006 02:04:56 -0000	1.3
***************
*** 1,3 ****
--- 1,4 ----
  package edu.whitman.halfway.util;
+ 
  // import cern.colt.function.DoubleDoubleFunction;
  import cern.colt.matrix.*;
***************
*** 6,77 ****
  // import cern.colt.list.DoubleArrayList;
  
- 
  import org.apache.log4j.Logger;
  
- 
  /** a dense factory that makes ElementAccessDenseDoubleMatrix2D's*/
! public class EADoubleFactory2D extends DoubleFactory2D{
!     static Logger log = Logger.getLogger(EADoubleFactory2D.class);
      
!     public DoubleMatrix2D make(DoubleMatrix1D m, int rows, int cols) {
! 	if(!(m instanceof EADoubleFactory1D.ElementAccessDenseDoubleMatrix1D)){
! 	    log.warn("Slow...");
! 	    m = (CernUtil.dense1D.make(m.size())).assign(m);
  
! 	}
! 	return new ElementAccessDenseDoubleMatrix2D
! 	    ( ((EADoubleFactory1D.ElementAccessDenseDoubleMatrix1D)m).getElements(), rows, cols);
  
!     }
  
  
  
!     public DoubleMatrix2D make(double[][] values) {
! 	return new ElementAccessDenseDoubleMatrix2D(values);
      }
  
!     public DoubleMatrix2D make(int rows, int columns) {
! 	return new ElementAccessDenseDoubleMatrix2D(rows, columns);
      }
  
!     public static class ElementAccessDenseDoubleMatrix2D 
! 	extends DenseDoubleMatrix2D{
! 
! 	public ElementAccessDenseDoubleMatrix2D(double[][] array){
! 	    super(array);
! 	}    
! 
! 	public ElementAccessDenseDoubleMatrix2D(int rows, int cols){
! 	    super(rows, cols);
! 	}
! 
! 
! 	/** elements is packed in row-major */
! 	public ElementAccessDenseDoubleMatrix2D(double[] elements, int rows, int cols){
! 	    super(rows, cols, elements, 0, 0, cols, 1);
! 	}    
!     
! 	public double[] getElements(){
! 	    return elements;
! 	}
! 
! 	public DoubleMatrix1D like1D(int size){
! 	    return new EADoubleFactory1D.ElementAccessDenseDoubleMatrix1D(size);
! 	}
  
! 	public DoubleMatrix2D like(int rows, int columns){
! 	    return new ElementAccessDenseDoubleMatrix2D(rows, columns);
! 	}
  
! 	protected DoubleMatrix1D like1D(int size, int zero, int stride) {
! 	    return new EADoubleFactory1D.ElementAccessDenseDoubleMatrix1D(size,this.elements,zero,stride);
! 	}
  
      }
  
  
  
  }
- 
- 
- 
--- 7,72 ----
  // import cern.colt.list.DoubleArrayList;
  
  import org.apache.log4j.Logger;
  
  /** a dense factory that makes ElementAccessDenseDoubleMatrix2D's*/
! public class EADoubleFactory2D extends DoubleFactory2D {
!   static Logger log = Logger.getLogger(EADoubleFactory2D.class);
! 
!   public DoubleMatrix2D make(DoubleMatrix1D m, int rows, int cols) {
!     if (!(m instanceof EADoubleFactory1D.ElementAccessDenseDoubleMatrix1D)) {
!       log.warn("Slow...");
!       m = (CernUtil.dense1D.make(m.size())).assign(m);
!       log.info("...done");
!     }
      
!     return new ElementAccessDenseDoubleMatrix2D(
!             ((EADoubleFactory1D.ElementAccessDenseDoubleMatrix1D) m)
!                     .getElements(), rows, cols);
  
!   }
  
!   public DoubleMatrix2D make(double[][] values) {
!     return new ElementAccessDenseDoubleMatrix2D(values);
!   }
  
+   public DoubleMatrix2D make(int rows, int columns) {
+     return new ElementAccessDenseDoubleMatrix2D(rows, columns);
+   }
  
+   public static class ElementAccessDenseDoubleMatrix2D extends
+           DenseDoubleMatrix2D {
  
!     public ElementAccessDenseDoubleMatrix2D(double[][] array) {
!       super(array);
      }
  
!     public ElementAccessDenseDoubleMatrix2D(int rows, int cols) {
!       super(rows, cols);
      }
  
!     /** elements is packed in row-major */
!     public ElementAccessDenseDoubleMatrix2D(double[] elements, int rows,
!             int cols) {
!       super(rows, cols, elements, 0, 0, cols, 1);
!     }
  
!     public double[] getElements() {
!       return elements;
!     }
  
!     public DoubleMatrix1D like1D(int size) {
!       return new EADoubleFactory1D.ElementAccessDenseDoubleMatrix1D(size);
!     }
  
+     public DoubleMatrix2D like(int rows, int columns) {
+       return new ElementAccessDenseDoubleMatrix2D(rows, columns);
      }
  
+     protected DoubleMatrix1D like1D(int size, int zero, int stride) {
+       return new EADoubleFactory1D.ElementAccessDenseDoubleMatrix1D(size,
+               this.elements, zero, stride);
+     }
  
+   }
  
  }