[Jigs-commits] CVS: jigs/src/edu/whitman/halfway/util TimingTree.java, NONE, 1.1 Timing.java, 1.1,

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Update of /cvsroot/jigs/jigs/src/edu/whitman/halfway/util
In directory sc8-pr-cvs6.sourceforge.net:/tmp/cvs-serv3714/src/edu/whitman/halfway/util

Modified Files:
	Timing.java MiscUtil.java StringUtil.java FileUtil.java 
	CernUtil.java 
Added Files:
	TimingTree.java 
Log Message:

--- NEW FILE: TimingTree.java ---
package edu.whitman.halfway.util;

import java.util.*;

import org.apache.log4j.Logger;

import cern.colt.matrix.ObjectFactory2D;
import cern.colt.matrix.ObjectMatrix2D;

public class TimingTree {
  protected static Logger log = Logger.getLogger(TimingTree.class);

  /**
   * As with the static instance in the Timing class, use with care.
   */
  public static TimingTree tt = new TimingTree();

  protected Node root = null;
  protected Node activeNode = null;

  /** Creates and starts the root timer */
  public TimingTree(){
    this.root = new Node("root", null);
    this.activeNode = root;    
  }

  public static void setStaticInstance(TimingTree t){
    TimingTree.tt = t;
  }

  public void start(String name){
    activeNode = activeNode.start(name);    
  }

  public ExecutionTimer getTimer(String dottedName){
    String[] name = dottedName.split(".");
    Node node = root;
    for(int i=0; i<name.length; i++){
      node = (Node) node.children.get(name);
      if(node == null){
        log.warn("Not timer of name " + dottedName);
        return null;
      }
    }
    return node.timer;
  }

  protected void incTime(long ms){
    activeNode.timer.incTime(ms);
    Node parent = activeNode.parent;
    while(parent != null){
      parent.timer.incTime(ms);
      parent = parent.parent;
    }
  }

  protected void incTimeRand(){
    long time = MiscUtil.randLongInRange(0, 999);//ms
    if(MiscUtil.randDoubleInRange(0, 1) < 0.9){//sec
      time += MiscUtil.randLongInRange(0, 59) * 1000;
    }
    if(MiscUtil.randDoubleInRange(0, 1) < 0.8){//min
      time += MiscUtil.randLongInRange(0, 59) * 1000*60;
    }
    if(MiscUtil.randDoubleInRange(0, 1) < 0.10){//h
      time += MiscUtil.randLongInRange(0, 5) * 1000*60*60;
    }
    incTime(time);
  }

  public boolean areTimersRunning(){
    return (activeNode != root);
  }

  public String stopAndPop(){
    if(activeNode == root){
      throw new IllegalArgumentException("Can't stop the root!");
    }
    String stoppedName = activeNode.name;
    activeNode.timer.stop();
    activeNode = activeNode.parent;
    return stoppedName;
  }

  public String stopAndPop(String name){
    if(!name.equals(activeNode.name)){
      log.warn(String.format("You're stopping %s, not %s like you thought.", activeNode.name, name));
    }
    return stopAndPop();
  }

  ArrayList nameCol, timeCol;
  public String toString(){
    return toString(false);
  }

  public String toString(boolean printZeros){
    nameCol = new ArrayList();
    timeCol = new ArrayList();
    StringBuffer sb = new StringBuffer();
    ArrayList childList = new ArrayList(root.children.keySet());   
    Collections.sort(childList);
    for(Object childName : childList){
      Node child = (Node)root.children.get(childName);
      buildString(child, 0, printZeros);
    }
    ObjectMatrix2D stringMatrix = ObjectFactory2D.dense.make(nameCol.size(),2);
    for(int i=0; i<nameCol.size(); i++){
      stringMatrix.set(i, 0, nameCol.get(i));
      stringMatrix.set(i, 1, timeCol.get(i));
    }
    cern.colt.matrix.objectalgo.Formatter objFormatter 
      = new cern.colt.matrix.objectalgo.Formatter();
    //objFormatter.setAlignment(Formatter.RIGHT);
    objFormatter.setPrintShape(false);
    return objFormatter.toString(stringMatrix);
  }

  protected long buildString(Node node, int depth, boolean printZeros){
    //depth first pre-order traversal
    nameCol.add(pad(depth) + node.name);
    timeCol.add(pad(depth) + "|" + StringUtil.formatMillis(
            node.timer.getElapsedTime(), printZeros));

    long totalChildrenTime = 0;
    ArrayList childList = new ArrayList(node.children.keySet());   
    Collections.sort(childList);
    for(Object childName : childList){
      Node child = (Node)node.children.get(childName);
      totalChildrenTime += buildString(child, depth+1, printZeros);
    }
    if(childList.size() > 0){
      nameCol.add(pad(depth+1) + "[overhead]");
      long overhead = node.timer.getElapsedTime() - totalChildrenTime;
      timeCol.add(pad(depth+1) + "|" + StringUtil.formatMillis(overhead, printZeros));
    }
    return node.timer.getElapsedTime();
  }

  protected String pad(int depth){
    StringBuffer sb = new StringBuffer();
    for(int i=0; i<depth; i++){
      sb.append("   ");
    }
   return sb.toString();
  }

  /** Takes a list of TimingTrees and returns a tree that is the "sum" of 
   * timings across same-name timiers. 
   * 
   * Note: Sums times over the union of the trees: eg, sum has a leaf if any of
   * the timers have such a leaf.
   * 
   * All timers should be stopped.
   * 
   * */ 
  public static TimingTree sum(List trees){
    TimingTree sumTT = new TimingTree();
    List roots = new ArrayList();
    for(Object tree : trees){
      roots.add(((TimingTree)tree).root);      
    }
    sumNodeAndRecurse(sumTT.root, roots);
    return sumTT;
  }

  protected static void sumNodeAndRecurse(Node sumNode, List nodesToSum){
    long time = 0;
    Map childListMap = new HashMap(); //map from String name -> Nodes of that name

    // calculate time for sumNode in the sumTree, and
    // create a list of all children of each name 
    for(Object nodeObj : nodesToSum){
      Node node = (Node) nodeObj;
      time += node.timer.getElapsedTime();
      //if(node.timer.isRunning()){
        //log.warn("Error, running timer " + node.name);
      //}
      for(Object childKey : node.children.keySet()){
        if(!childListMap.containsKey(childKey)){
          childListMap.put(childKey, new ArrayList());
        }        
        ArrayList listForName = (ArrayList) childListMap.get(childKey);
        listForName.add(node.children.get(childKey));
      }      
    }
    sumNode.timer.incTime(time);

    for(Object entryObj : childListMap.entrySet()){
      Map.Entry entry = (Map.Entry) entryObj;
      String childKey = (String) entry.getKey();
      List childNodeList = (List)entry.getValue();
      Node sumChild = sumNode.getOrCreateChild(childKey);
      sumNodeAndRecurse(sumChild, childNodeList);      
    }       
  }

  class Node{
    String name;
    ExecutionTimer timer;
    Node parent;
    Map children;  // maps String name -> Node child

    protected Node(String name, Node parent){
      this.parent = parent;
      this.name = name;
      this.timer = new ExecutionTimer(name);
      this.children = new HashMap();
    }

    protected Node start(String name){
      Node child = getOrCreateChild(name);
      assert !child.timer.isRunning();
      child.timer.start();
      return child;
    }

    protected Node getOrCreateChild(String name){
      if(children.containsKey(name)){
        return (Node) children.get(name);
      }else{
        Node child = new Node(name, this);
        children.put(name, child);
        return child;
      }
    }

  }

  public static TimingTree getSampleTree(){
    TimingTree tt = new TimingTree();
    tt.start("root task 1");
    tt.start("subroutine");    
    tt.start("super-sub"); tt.incTimeRand();
    tt.stopAndPop();tt.incTimeRand();
    tt.start("equally super sub");tt.incTimeRand();
    tt.stopAndPop();tt.incTimeRand();
    tt.stopAndPop();tt.incTimeRand();
    tt.start("subroutine 2");tt.incTimeRand();tt.incTimeRand();
    tt.stopAndPop();tt.incTimeRand();
    tt.stopAndPop();tt.incTimeRand();
    tt.start("root task 2");tt.incTimeRand();
    tt.stopAndPop();
    return tt;
  }

  public static void test(){
   System.out.println("Timer One:");   
   TimingTree tt1 = getSampleTree();
   assert(!tt1.areTimersRunning());
   System.out.println(tt1);

   System.out.println();
   System.out.println("Timer Two:");   
   TimingTree tt2 = getSampleTree();
   assert(!tt2.areTimersRunning());
   System.out.println(tt2);
   System.out.println();
   System.out.println();

   ArrayList trees = new ArrayList(2);
   trees.add(tt1); trees.add(tt2);
   TimingTree ttSum = TimingTree.sum(trees);
   assert(!ttSum.areTimersRunning());
   System.out.println(ttSum); 
  }

}

Index: Timing.java
===================================================================
RCS file: /cvsroot/jigs/jigs/src/edu/whitman/halfway/util/Timing.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Timing.java	10 Aug 2006 22:53:35 -0000	1.1
--- Timing.java	29 Aug 2006 19:29:56 -0000	1.2
***************
*** 28,32 ****
    protected static Logger log = Logger.getLogger(Timing.class);

!   public static Timing t = new Timing();
    protected Map map = new HashMap();

--- 28,32 ----
    protected static Logger log = Logger.getLogger(Timing.class);

!   private static Timing t = new Timing();
    protected Map map = new HashMap();

Index: MiscUtil.java
===================================================================
RCS file: /cvsroot/jigs/jigs/src/edu/whitman/halfway/util/MiscUtil.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** MiscUtil.java	6 Aug 2006 19:02:46 -0000	1.22
--- MiscUtil.java	29 Aug 2006 19:29:56 -0000	1.23
***************
*** 822,825 ****
--- 822,831 ----

+     public final static boolean isNonNegative(double[] a){
+       for(double v : a){
+         if( v < 0) return false;
+       }
+       return true;
+     }

      /** Checks that the values in dist sum to 1 (within 10e-6) */
***************
*** 827,830 ****
--- 833,837 ----
          double sum = 0;
          for(int i=0; i< dist.length; i++){
+             if(dist[i] < 0) return false;
              sum += dist[i];
          }

Index: StringUtil.java
===================================================================
RCS file: /cvsroot/jigs/jigs/src/edu/whitman/halfway/util/StringUtil.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** StringUtil.java	10 Aug 2006 22:53:35 -0000	1.12
--- StringUtil.java	29 Aug 2006 19:29:56 -0000	1.13
***************
*** 7,317 ****
  import org.apache.oro.text.regex.*;

! public final class StringUtil{
!     public static final String newline = System.getProperty("line.separator");
!     
!     static PatternMatcher matcher = new Perl5Matcher();
!     static PatternCompiler compiler = new Perl5Compiler();
!     static Perl5Util regxp = new Perl5Util();

!     static Logger log = Logger.getLogger(StringUtil.class.getName());

!     
!     public static final String formatMillis(long ms){
!       String w = "    ";
!       long totalMillis = ms;
!       long sec = ms / 1000;
!       ms = ms % 1000;
!       if(sec == 0){
!         return String.format("%s%s%s %03dms",w,w,w, ms);
!       }
!       long min = sec / 60;
!       sec = sec % 60;
!       if (min ==0){
!         return String.format("%s%s%02ds  %03dms",w,w, sec, ms);
!       }
!       long hr = min / 60;
!       min = min % 60;
!       if (hr == 0){
!         return String.format("%s%02dm:%02ds  %03dms", w, min, sec, ms);
!       }
!       
!       assert 60*60*1000*hr + 60*1000*min + 1000*sec + ms == totalMillis;
!       
!       
!       return String.format("%dh:%02dm:%02ds  %03dms", hr, min, sec, ms);
!       
      }

!     public static final String stripLeadingNumsUnderscore(String s){
!         return regxp.substitute("s/^[0-9]+_//", s);
      }

!     /** Returns true if the string is non-null and non-whitespace */
!     public static final boolean hasContents(String s){
!         if(s==null) return false;
!         return  !s.trim().equals("");
!     }    

!     /** Returns a representation of the current time without any
!      * spaces, usefull for use in temprorary file names, etc.
!      The format is month-day-year_[hr]h-[min]m
!     */
!     public static final String timeForFile(){
!         Calendar c = Calendar.getInstance();
!         
!         return c.get(c.MONTH) + "-" +
!             c.get(c.DAY_OF_MONTH) + "-" +
!             c.get(c.YEAR) + "_" +
!             c.get(c.HOUR_OF_DAY) +"h-" +
!             c.get(c.MINUTE) + "m";
!     }

!     public static String readToString(InputStream in){
!         StringBuffer sb = new StringBuffer();
!         try{
!             BufferedReader inbr = new BufferedReader(new InputStreamReader(in));
!             String line;
!             while((line = inbr.readLine() )!=null){
!                 sb.append(line);
!             }
!         }catch(IOException e){
!             log.error("IOException while reading from stream " + in+ " to String.",  e);
!             return null;
!         }
! 	
!         return sb.toString();
      }

!     /** replaces all occurence of the "key" strings with the "value"
!      * string in target String*/
!     public static final String simpleReplace(Map oldNew, String target){
!         Set entries = oldNew.entrySet();
!         Iterator iter = entries.iterator();
!         while(iter.hasNext()){
!             Map.Entry en = (Map.Entry)iter.next();
!             String key = (String)en.getKey();
!             String val = (String)en.getValue();
!             target = simpleReplace(target, key, val);            
!         }
!         return target;
      }

!     //replaces all occurences of old with subsValue in string
!     public static final String simpleReplace(String string, String old, String subsValue){
!         try{
!             return Util.substitute
!                 (matcher,
!                  compiler.compile(Perl5Compiler.quotemeta(old)),
!                  new StringSubstitution(subsValue),
!                  string,
!                  Util.SUBSTITUTE_ALL );
!         }catch(MalformedPatternException e){
!             log.error("Error substituting for " + old + StringUtil.newline +
!                       " with subs value: " + StringUtil.newline + subsValue, e);
!             return null;
!         }
      }

! 
!     public static AbstractList tokenize(String string){
!         StringTokenizer st = new StringTokenizer(string);
!         ArrayList tokens = new ArrayList();
!         while(st.hasMoreTokens()){
!             tokens.add(st.nextToken());
!         }
!         return tokens;
      }

!     
!     /** Tokenizes the string, treating strings quoted with " as a
!      * single entry.  Also parses numbers.  The resulting List thus
!      * has Strings and Doubles. Returns null if parsing fails.*/
!     public static AbstractList tokenizeWithQuotes(String string){
!         // StreamTokenizer seems to be pretty badly broken ... it
!         // won't parse strings like "../CMU/Climbing" if number
!         // parsing is disabled. so we reset everything, make
!         // everything except whitespace word characters.  then, for
!         // each word we try to parse it as a double, and if that
!         // succeeds we keep it as a double, if not we put the string
!         // in the list.
! 	
! 
!         try{
!             StringReader reader = new StringReader(string);
!             StreamTokenizer st = new StreamTokenizer(reader);
!             st.resetSyntax();
!             st.wordChars(0,255);
!             st.whitespaceChars(0, ' ');
!             st.quoteChar('"');
!             st.slashSlashComments(false);
!             st.slashStarComments(false); 
!             LinkedList tokens = new LinkedList();
!             while(st.nextToken() != StreamTokenizer.TT_EOF){
!                 if(st.ttype == StreamTokenizer.TT_WORD || st.ttype == '"'){
!                     log.debug("Read Word or Quote" + st.sval);
!                     String s = st.sval;
!                     Double d = makeDouble(s);
!                     tokens.add( (d == null) ? (Object)s : (Object)d );
!                 }else{//single character, convert to string and add
!                     char c = (char)st.ttype;
!                     log.warn("Got unexpected ttype " + st.ttype + " " + c+ ", sval = " + st.sval +", nval = " + st.nval);
!                 }
!             }
!             return tokens;
!         }catch(IOException e){
!             log.error("tokenizing failed", e);
!             return null;
!         }
!     } 
!     

!     /** Prefixes the string input with enough copies of pad that it
!         has length equal to length.  Returns null and logs an error if
!         padding with pad cannot produce a string of exactly length.
!         Usually, pad should be a single character.*/
!     public static String pad(String input, int length, String pad){
!         StringBuffer sb = new StringBuffer();
!         int padLength = length - input.length();
!         while(sb.length() < padLength){
!             sb.append(pad);
!         }
!         sb.append(input);
!         if(sb.length() != length){
!             log.error("Could not pad \"" + input +"\" with \"" + pad +"\" to get length " + length);
!             return null;
          }
!         return sb.toString();

      }

!     // --------------- Convert Objects to Strings, etc -------------------- //
!     
!     /**
!        Takes an object input and makes an appropriate string, which can then 
!        be placed in the properties class. If the class type is unknown, 
!        returns the null string.

!        @deprecated Use ObjectSerializer;
!     */
!     public static String getObjectsString(Object o){
!         return ObjectSerializer.getStringForObject(o);
!     }

!     /**
!        Takes the string input and tries to make it an instance of
!        type.  If type is primitive, tries to create the appropriate
!        wrapped object.  Returns null if input is null, if input is
!        "null", or if some error in conversion occurs.  

!        @deprecated Use ObjectSerializer;
!     */
!     
!     public static Object makeStringObject(String input){
!         return ObjectSerializer.getObjectForString(input);
!     }

!     // --------------- String Conversion Methods --------------- //

!     public static Integer makeInteger(String s){
!         if(s==null) return null;
!         Integer rval = null;
!         try{
!             rval = new Integer(s);
!         }catch(NumberFormatException e){
!             return null;
!         }
!         return rval;
!     }

!     public static Short makeShort(String s){
!         if(s==null) return null;
!         Short rval = null;
!         try{
!             rval = new Short(s);
!         }catch(NumberFormatException e){
!             return null;
!         }
!         return rval;
      }

!     public static Long makeLong(String s){
!         if(s==null) return null;
!         Long rval = null;
!         try{
!             rval = new Long(s);
!         }catch(NumberFormatException e){
!             return null;
!         }
!         return rval;
      }

!     public static Float makeFloat(String s){
!         if(s==null) return null;
!         Float rval = null;
!         try{
!             rval = new Float(s);
!         }catch(NumberFormatException e){
!             return null;
!         }
!         return rval;
      }

!     public static Double makeDouble(String s){
!         if(s==null) return null;
!         Double rval = null;
!         try{
!             rval = new Double(s);
!         }catch(NumberFormatException e){
!             return null;
!         }
!         return rval;
      }
! 	
!     public static Boolean makeBoolean(String s){
!         if(s==null) return null;
!         s=s.trim();
!         if(s.equalsIgnoreCase("true")
!            || s.equalsIgnoreCase("yes")
!            || s.equalsIgnoreCase("1") )
!             {
!                 return new Boolean(true);
!             }else{ 
!                 return new Boolean(false);
!             }
      }

!     public static Byte makeByte(String s){
!         if(s==null) return null;
!         Byte rval;
!         try{
!             rval = new Byte(s);
!         }catch(NumberFormatException e){
!             return null;
!         }
!         return rval;
      }

!     public static Character makeCharacter(String s){
!         if(s==null) return null;
!         if(s.length() != 1) return null;
!         return new Character(s.charAt(0));
      }

!     public static void main(String[] args){
!       long[] times = { 100, 13011,
!                        60*60*1000*59 + 60*1000*32 + 1000*49 + 333,
!                        60*60*1000*0 + 60*1000*32 + 1000*49 + 333,
!                        60*60*1000*0 + 60*1000*0 + 1000*49 + 3,
!                        60*60*1000*90 + 60*1000*0 + 1000*49 + 3,
!       };
!       for (long t : times){
!         System.out.println(StringUtil.formatMillis(t));
!       }      
      }
!     

  }
--- 7,333 ----
  import org.apache.oro.text.regex.*;

! public final class StringUtil {
!   public static final String newline = System.getProperty("line.separator");

!   static PatternMatcher matcher = new Perl5Matcher();
!   static PatternCompiler compiler = new Perl5Compiler();
!   static Perl5Util regxp = new Perl5Util();

!   static Logger log = Logger.getLogger(StringUtil.class.getName());
! 
!   public static final String formatMemory(long bytes){
!     String format = "%.2f";
!     double bytesD = bytes;
!     if(bytesD < 1024){
!       return String.format(format + " B", bytesD);     
!     }else if (bytesD < 1024*1024){
!       return String.format(format + " KB", bytesD/1024);
!     }else if(bytesD < 1024*1024*1024){
!       return String.format(format + " MB", bytesD/(1024*1024));
!     }else{
!       return String.format(format + " GB", bytesD/(1024*1024*1024));
!     }    
!   }
!   
!   public static final String formatMillis(long ms){
!    return formatMillis(ms, false);
!   }
!   
!   public static final String formatMillis(long ms, boolean printZeros) {
!     String w = "    ";
!     long totalMillis = ms;
!     long sec = ms / 1000;
!     ms = ms % 1000;
!     if (sec == 0 && !printZeros) {
!       return String.format("%s%s%s %03dms", w, w, w, ms);
!     }
!     long min = sec / 60;
!     sec = sec % 60;
!     if (min == 0 && !printZeros) {
!       return String.format("%s%s%02ds  %03dms", w, w, sec, ms);
!     }
!     long hr = min / 60;
!     min = min % 60;
!     if (hr == 0 && !printZeros) {
!       return String.format("%s%02dm:%02ds  %03dms", w, min, sec, ms);
      }

!     assert 60 * 60 * 1000 * hr + 60 * 1000 * min + 1000 * sec + ms == totalMillis;
! 
!     if(!printZeros){    
!       return String.format("%2dh:%02dm:%02ds  %03dms", hr, min, sec, ms);
!     }else{
!       return String.format("%02dh:%02dm:%02ds  %03dms", hr, min, sec, ms);
      }

!   }

+   public static final String stripLeadingNumsUnderscore(String s) {
+     return regxp.substitute("s/^[0-9]+_//", s);
+   }

!   /** Returns true if the string is non-null and non-whitespace */
!   public static final boolean hasContents(String s) {
!     if (s == null)
!       return false;
!     return !s.trim().equals("");
!   }

+   /** Returns a representation of the current time without any
+    * spaces, usefull for use in temprorary file names, etc.
+    The format is month-day-year_[hr]h-[min]m
+    */
+   public static final String timeForFile() {
+     Calendar c = Calendar.getInstance();

!     return c.get(c.MONTH) + "-" + c.get(c.DAY_OF_MONTH) + "-" + c.get(c.YEAR)
!             + "_" + c.get(c.HOUR_OF_DAY) + "h-" + c.get(c.MINUTE) + "m";
!   }
! 
!   public static String readToString(InputStream in) {
!     StringBuffer sb = new StringBuffer();
!     try {
!       BufferedReader inbr = new BufferedReader(new InputStreamReader(in));
!       String line;
!       while ((line = inbr.readLine()) != null) {
!         sb.append(line);
!       }
!     } catch (IOException e) {
!       log.error("IOException while reading from stream " + in + " to String.",
!               e);
!       return null;
      }

+     return sb.toString();
+   }

!   /** replaces all occurence of the "key" strings with the "value"
!    * string in target String*/
!   public static final String simpleReplace(Map oldNew, String target) {
!     Set entries = oldNew.entrySet();
!     Iterator iter = entries.iterator();
!     while (iter.hasNext()) {
!       Map.Entry en = (Map.Entry) iter.next();
!       String key = (String) en.getKey();
!       String val = (String) en.getValue();
!       target = simpleReplace(target, key, val);
      }
+     return target;
+   }

!   //replaces all occurences of old with subsValue in string
!   public static final String simpleReplace(String string, String old,
!           String subsValue) {
!     try {
!       return Util.substitute(matcher, compiler.compile(Perl5Compiler
!               .quotemeta(old)), new StringSubstitution(subsValue), string,
!               Util.SUBSTITUTE_ALL);
!     } catch (MalformedPatternException e) {
!       log.error("Error substituting for " + old + StringUtil.newline
!               + " with subs value: " + StringUtil.newline + subsValue, e);
!       return null;
      }
+   }

!   public static AbstractList tokenize(String string) {
!     StringTokenizer st = new StringTokenizer(string);
!     ArrayList tokens = new ArrayList();
!     while (st.hasMoreTokens()) {
!       tokens.add(st.nextToken());
      }
+     return tokens;
+   }

!   /** Tokenizes the string, treating strings quoted with " as a
!    * single entry.  Also parses numbers.  The resulting List thus
!    * has Strings and Doubles. Returns null if parsing fails.*/
!   public static AbstractList tokenizeWithQuotes(String string) {
!     // StreamTokenizer seems to be pretty badly broken ... it
!     // won't parse strings like "../CMU/Climbing" if number
!     // parsing is disabled. so we reset everything, make
!     // everything except whitespace word characters.  then, for
!     // each word we try to parse it as a double, and if that
!     // succeeds we keep it as a double, if not we put the string
!     // in the list.

!     try {
!       StringReader reader = new StringReader(string);
!       StreamTokenizer st = new StreamTokenizer(reader);
!       st.resetSyntax();
!       st.wordChars(0, 255);
!       st.whitespaceChars(0, ' ');
!       st.quoteChar('"');
!       st.slashSlashComments(false);
!       st.slashStarComments(false);
!       LinkedList tokens = new LinkedList();
!       while (st.nextToken() != StreamTokenizer.TT_EOF) {
!         if (st.ttype == StreamTokenizer.TT_WORD || st.ttype == '"') {
!           log.debug("Read Word or Quote" + st.sval);
!           String s = st.sval;
!           Double d = makeDouble(s);
!           tokens.add((d == null) ? (Object) s : (Object) d);
!         } else {//single character, convert to string and add
!           char c = (char) st.ttype;
!           log.warn("Got unexpected ttype " + st.ttype + " " + c + ", sval = "
!                   + st.sval + ", nval = " + st.nval);
          }
!       }
!       return tokens;
!     } catch (IOException e) {
!       log.error("tokenizing failed", e);
!       return null;
!     }
!   }

+   /** Prefixes the string input with enough copies of pad that it
+    has length equal to length.  Returns null and logs an error if
+    padding with pad cannot produce a string of exactly length.
+    Usually, pad should be a single character.*/
+   public static String pad(String input, int length, String pad) {
+     StringBuffer sb = new StringBuffer();
+     int padLength = length - input.length();
+     while (sb.length() < padLength) {
+       sb.append(pad);
+     }
+     sb.append(input);
+     if (sb.length() != length) {
+       log.error("Could not pad \"" + input + "\" with \"" + pad
+               + "\" to get length " + length);
+       return null;
      }
+     return sb.toString();

!   }

!   // --------------- Convert Objects to Strings, etc -------------------- //

!   /**
!    Takes an object input and makes an appropriate string, which can then 
!    be placed in the properties class. If the class type is unknown, 
!    returns the null string.

!    @deprecated Use ObjectSerializer;
!    */
!   public static String getObjectsString(Object o) {
!     return ObjectSerializer.getStringForObject(o);
!   }

+   /**
+    Takes the string input and tries to make it an instance of
+    type.  If type is primitive, tries to create the appropriate
+    wrapped object.  Returns null if input is null, if input is
+    "null", or if some error in conversion occurs.  

!    @deprecated Use ObjectSerializer;
!    */

!   public static Object makeStringObject(String input) {
!     return ObjectSerializer.getObjectForString(input);
!   }

!   // --------------- String Conversion Methods --------------- //
! 
!   public static Integer makeInteger(String s) {
!     if (s == null)
!       return null;
!     Integer rval = null;
!     try {
!       rval = new Integer(s);
!     } catch (NumberFormatException e) {
!       return null;
      }
+     return rval;
+   }

!   public static Short makeShort(String s) {
!     if (s == null)
!       return null;
!     Short rval = null;
!     try {
!       rval = new Short(s);
!     } catch (NumberFormatException e) {
!       return null;
      }
+     return rval;
+   }

!   public static Long makeLong(String s) {
!     if (s == null)
!       return null;
!     Long rval = null;
!     try {
!       rval = new Long(s);
!     } catch (NumberFormatException e) {
!       return null;
      }
+     return rval;
+   }

!   public static Float makeFloat(String s) {
!     if (s == null)
!       return null;
!     Float rval = null;
!     try {
!       rval = new Float(s);
!     } catch (NumberFormatException e) {
!       return null;
      }
!     return rval;
!   }
! 
!   public static Double makeDouble(String s) {
!     if (s == null)
!       return null;
!     Double rval = null;
!     try {
!       rval = new Double(s);
!     } catch (NumberFormatException e) {
!       return null;
      }
+     return rval;
+   }

!   public static Boolean makeBoolean(String s) {
!     if (s == null)
!       return null;
!     s = s.trim();
!     if (s.equalsIgnoreCase("true") || s.equalsIgnoreCase("yes")
!             || s.equalsIgnoreCase("1")) {
!       return new Boolean(true);
!     } else {
!       return new Boolean(false);
      }
+   }

!   public static Byte makeByte(String s) {
!     if (s == null)
!       return null;
!     Byte rval;
!     try {
!       rval = new Byte(s);
!     } catch (NumberFormatException e) {
!       return null;
      }
+     return rval;
+   }

!   public static Character makeCharacter(String s) {
!     if (s == null)
!       return null;
!     if (s.length() != 1)
!       return null;
!     return new Character(s.charAt(0));
!   }
! 
!   public static void main(String[] args) {
!     long[] times = { 100, 13011,
!             60 * 60 * 1000 * 59 + 60 * 1000 * 32 + 1000 * 49 + 333,
!             60 * 60 * 1000 * 0 + 60 * 1000 * 32 + 1000 * 49 + 333,
!             60 * 60 * 1000 * 0 + 60 * 1000 * 0 + 1000 * 49 + 3,
!             60 * 60 * 1000 * 90 + 60 * 1000 * 0 + 1000 * 49 + 3, };
!     for (long t : times) {
!       System.out.println(StringUtil.formatMillis(t));
      }
!   }

  }

Index: FileUtil.java
===================================================================
RCS file: /cvsroot/jigs/jigs/src/edu/whitman/halfway/util/FileUtil.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** FileUtil.java	2 Aug 2006 21:36:16 -0000	1.13
--- FileUtil.java	29 Aug 2006 19:29:56 -0000	1.14
***************
*** 129,136 ****
      }

      public static boolean writeObjectToFile(File f, Serializable object){
          try{
              FileOutputStream ostream = new FileOutputStream(f);
!             ObjectOutputStream p = new ObjectOutputStream(ostream);
              p.writeObject(object);
              p.flush();
--- 129,151 ----
      }

+     public static boolean writeToFile(File f, double[] data){
+       try {
+         Writer out = new FileWriter(f);
+         for(int i=0; i<data.length; i++){
+           out.write(String.format("%.15g%n", data[i]));
+         }
+         out.close();
+       } catch (IOException e) {
+         log.warn("Error writing array to file " + f, e);
+         return false;
+       }
+       return true;
+     }
+     
+     
      public static boolean writeObjectToFile(File f, Serializable object){
          try{
              FileOutputStream ostream = new FileOutputStream(f);
!             ObjectOutputStream p = new ObjectOutputStream(new BufferedOutputStream(ostream));
              p.writeObject(object);
              p.flush();
***************
*** 389,392 ****
--- 404,409 ----
      }

+ 
+     
      public static DoubleArrayList readToDoubleArray(File f){
          try{

Index: CernUtil.java
===================================================================
RCS file: /cvsroot/jigs/jigs/src/edu/whitman/halfway/util/CernUtil.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** CernUtil.java	29 Mar 2005 20:53:59 -0000	1.11
--- CernUtil.java	29 Aug 2006 19:29:56 -0000	1.12
***************
*** 3,6 ****
--- 3,7 ----
  import cern.colt.matrix.*;
  //import cern.colt.matrix.impl.*;
+ import cern.colt.matrix.impl.RCDoubleMatrix2D;
  import cern.colt.matrix.linalg.Algebra;
  import cern.colt.list.DoubleArrayList;
***************
*** 11,14 ****
--- 12,20 ----
  import java.io.*;

+ import no.uib.cipr.matrix.Matrix;
+ import no.uib.cipr.matrix.MatrixEntry;
+ import no.uib.cipr.matrix.Vector;
+ import no.uib.cipr.matrix.VectorEntry;
+ 
  import org.apache.log4j.Logger;

***************
*** 18,25 ****
  public final class CernUtil{

-   
      private static Logger log = Logger.getLogger(CernUtil.class);
- 
- 
      private static cern.jet.math.Functions F = cern.jet.math.Functions.functions;
      private static Algebra linalg = new Algebra();
--- 24,28 ----
***************
*** 32,35 ****
--- 35,73 ----

+     public static final String densityStatString(String prefix, 
+             DoubleMatrix1D vector, double approxThresh){
+       StringBuffer sb = new StringBuffer(prefix);
+       double fracNonzero = fractionNonzero(vector);
+       sb.append(String.format("%.3f%% nonzero", fracNonzero*100.0));
+       if(approxThresh != 0){
+         double approxNonzero = fractionNonzero(vector, approxThresh);
+         sb.append(String.format(", %.3f%% approx nonzero", 
+                 approxNonzero*100));
+       }
+       return sb.toString();
+     }
+     
+     
+     /** 
+      * Note sure how efficient this actually is.
+      * @param m
+      * @return
+      */
+     public static final DoubleMatrix2D makeRC(Matrix m){
+       DoubleMatrix2D m2 = DoubleFactory2D.rowCompressed.make(m.numRows(), m.numColumns());
+       for(MatrixEntry me : m){
+         m2.set(me.row(), me.column(), me.get());
+       }      
+       return m2;
+     }
+     
+     public static final DoubleMatrix1D makeSparse(Vector v){
+         DoubleMatrix1D nv = DoubleFactory1D.sparse.make(v.size());
+         for(VectorEntry ve : v){
+           nv.set(ve.index(), ve.get());
+         }
+         return nv;      
+     }
+     
      /* the bins are 1, ..., numBins (not 0, ... , numBins-1) so we can
       * use sparsity as a mask.*/
***************
*** 90,93 ****
--- 128,138 ----
      }

+     public static final int minNonzeroIndex(DoubleMatrix1D a){
+       IntArrayList indexList = new IntArrayList();
+       a.getNonZeros(indexList, null);
+       indexList.sort();
+       return indexList.get(0);      
+     }
+     
      protected static final boolean sanityCheckBins(DoubleMatrix2D in, DoubleMatrix2D out, int numBins){
          int nr = in.rows();
***************
*** 166,169 ****
--- 211,236 ----
      }

+     public static final double fractionNonzero(DoubleMatrix1D a){
+       return fractionNonzero(a, 0.0);
+     }
+     
+     public static final double fractionNonzero(DoubleMatrix1D a, double epsilon){
+       if(epsilon == 0.0){
+         return (double)a.cardinality()/a.size();
+       }else{
+         DoubleArrayList valueList = new DoubleArrayList(0);
+         a.getNonZeros(null, valueList);
+         int nnz = valueList.size();
+         double count = 0;
+         for(int i = 0; i<nnz; i++){
+           double v = valueList.get(i);
+           if(v > epsilon || v < -epsilon){
+             count ++;
+           }
+         }
+         return count/(double)a.size();
+       }      
+     }
+     
      public static final double maxIgnoreZero(DoubleMatrix1D a){
          int n = a.size();

[Jigs-commits] CVS: jigs/src/edu/whitman/halfway/util TimingTree.java, NONE, 1.1 Timing.java, 1.1,

[Jigs-commits] CVS: jigs/src/edu/whitman/halfway/util TimingTree.java, NONE, 1.1 Timing.java, 1.1, 1.2 MiscUtil.java, 1.22, 1.23 StringUtil.java, 1.12, 1.13 FileUtil.java, 1.13, 1.14 CernUtil.java, 1.11, 1.12