Index: /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java =================================================================== --- /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (revision 1728) +++ /branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (revision 1729) @@ -79,8 +79,7 @@ */ public class SequenceForTaskDetectionRuleAlignment implements ISessionScopeRule { - - public static int nThreads = Runtime.getRuntime().availableProcessors()-1; - - + + public static int nThreads = Runtime.getRuntime().availableProcessors() - 1; + private int iteration = 0; /** @@ -98,5 +97,4 @@ */ private ITaskBuilder taskBuilder; - /** @@ -161,9 +159,9 @@ } } - + public RuleApplicationData loadAppData(String name) { String objectName = name; String filename = name + ".dat"; - + Object data = null; FileInputStream fis = null; @@ -182,7 +180,8 @@ CommandHelpers.dataOverwritten(objectName); } - return (RuleApplicationData) GlobalDataContainer.getInstance().getData(name); - } - + return (RuleApplicationData) GlobalDataContainer.getInstance().getData( + name); + } + /* * (non-Javadoc) @@ -195,34 +194,34 @@ public RuleApplicationResult apply(List sessions) { RuleApplicationData appData = new RuleApplicationData(sessions); - //File harmonized = new File("harmonized.dat"); - //if(harmonized.exists() && !harmonized.isDirectory()) { - // Console.traceln(Level.INFO,"loading harmonized sessions from file"); - // appData = loadAppData("harmonized"); - //} - //else { - //appData.getStopWatch().start("harmonization"); - harmonizeEventTaskInstancesModel(appData); - //appData.getStopWatch().stop("harmonization"); - GlobalDataContainer.getInstance().addData("harmonized", appData); - //Saving intermediate results to file - Console.traceln(Level.INFO,"saving substitution matrix to file"); - //saveAppData("harmonized"); - //} - - //File substitution = new File("substitution.dat"); - //if(!(substitution.exists() && !substitution.isDirectory())) { - Console.traceln(Level.INFO, "generating substitution matrix from " + appData.getUniqueTasks().size() + " unique tasks"); - appData.getStopWatch().start("substitution matrix"); - appData.getSubmat().generate(appData.getUniqueTasks()); - appData.getStopWatch().stop("substitution matrix"); - // GlobalDataContainer.getInstance().addData("substitution", appData); - // saveAppData("substitution"); - //} - //else { - // Console.traceln(Level.INFO,"loading substitution matrix from file"); - // appData = loadAppData("substitution"); - //} - - + // File harmonized = new File("harmonized.dat"); + // if(harmonized.exists() && !harmonized.isDirectory()) { + // Console.traceln(Level.INFO,"loading harmonized sessions from file"); + // appData = loadAppData("harmonized"); + // } + // else { + // appData.getStopWatch().start("harmonization"); + harmonizeEventTaskInstancesModel(appData); + // appData.getStopWatch().stop("harmonization"); + GlobalDataContainer.getInstance().addData("harmonized", appData); + // Saving intermediate results to file + Console.traceln(Level.INFO, "saving substitution matrix to file"); + // saveAppData("harmonized"); + // } + + // File substitution = new File("substitution.dat"); + // if(!(substitution.exists() && !substitution.isDirectory())) { + Console.traceln(Level.INFO, "generating substitution matrix from " + + appData.getUniqueTasks().size() + " unique tasks"); + appData.getStopWatch().start("substitution matrix"); + appData.getSubmat().generate(appData.getUniqueTasks()); + appData.getStopWatch().stop("substitution matrix"); + // GlobalDataContainer.getInstance().addData("substitution", appData); + // saveAppData("substitution"); + // } + // else { + // Console.traceln(Level.INFO,"loading substitution matrix from file"); + // appData = loadAppData("substitution"); + // } + Console.traceln(Level.INFO, "Starting main loop"); do { @@ -256,5 +255,4 @@ return appData.getResult(); } - private ArrayList createNumberSequences( @@ -531,5 +529,5 @@ * @return */ - public ISequence matchAsSequence(RuleApplicationData appData, Match m) { + public ISequence matchAsSequence(RuleApplicationData appData, Match m) { ISequence sequence = taskFactory.createNewSequence(); appData.newTaskCreated(sequence); @@ -598,5 +596,5 @@ taskBuilder.addChild(selection, subsequence1); taskBuilder.addChild(selection, subsequence2); - taskBuilder.addChild(sequence,selection); + taskBuilder.addChild(sequence, selection); while (i < first.length - 1 && selectionfound) { selectionfound = false; @@ -608,11 +606,10 @@ && second[i + 1] != -1) { selectionfound = true; - } - else{ + } else { continue; } i++; } - if(i==first.length-1 && selectionfound) { + if (i == first.length - 1 && selectionfound) { taskBuilder.addChild(subsequence1, appData .getNumber2Task().get(first[i])); @@ -621,6 +618,5 @@ } } - } - else { + } else { if ((first[i] != second[i])) { @@ -651,14 +647,15 @@ // Create NumberSequences appData.setNumberSequences(this.createNumberSequences(appData)); - + // Generate pairwise alignments - //appData.setMatchseqs(generatePairwiseAlignments(appData)); + // appData.setMatchseqs(generatePairwiseAlignments(appData)); generatePairwiseAlignments(appData); - //Searching each match in all other sessions, counting its occurences + // Searching each match in all other sessions, counting its occurences searchMatchesInAllSessions(appData); - + // Sort results to get the most occurring results - Console.traceln(Level.INFO, "sorting " + appData.getMatchseqs().size() + " results"); + Console.traceln(Level.INFO, "sorting " + appData.getMatchseqs().size() + + " results"); Comparator comparator = new Comparator() { public int compare(Match m1, Match m2) { @@ -667,5 +664,5 @@ } }; - + Collections.sort(appData.getMatchseqs(), comparator); appData.getStopWatch().stop("detecting tasks"); @@ -676,5 +673,5 @@ HashMap> replacedOccurences = new HashMap>(); for (int i = 0; i < appData.getMatchseqs().size(); i++) { - + // Every pattern consists of 2 sequences, therefore the minimum // occurrences here is 2. @@ -683,9 +680,11 @@ if (appData.getMatchseqs().get(i).occurenceCount() > 2) { appData.detectedAndReplacedTasks = true; - ISequence task = matchAsSequence(appData, appData.getMatchseqs().get(i)); - invalidOccurence: for (Iterator it = appData.getMatchseqs() - .get(i).getOccurences().iterator(); it.hasNext();) { + ISequence task = matchAsSequence(appData, appData + .getMatchseqs().get(i)); + invalidOccurence: for (Iterator it = appData + .getMatchseqs().get(i).getOccurences().iterator(); it + .hasNext();) { MatchOccurence oc = it.next(); - + // Check if nothing has been replaced in the sequence we // want to replace @@ -731,5 +730,6 @@ } } - System.out.println("Replacing in sequence" + oc.getSequenceId()); + System.out.println("Replacing in sequence" + + oc.getSequenceId()); ISequenceInstance sequenceInstances = RuleUtils .createNewSubSequenceInRange(appData.getSessions() @@ -746,30 +746,35 @@ } } - //appData.setMatchseqs(null); + // appData.setMatchseqs(null); appData.getStopWatch().stop("replacing tasks"); } - - - + + private void replaceMatches() { + + } private void searchMatchesInAllSessions(RuleApplicationData appData) { - Console.traceln(Level.INFO, "searching for patterns occuring most with " + nThreads + " threads"); - //Prepare parallel search of matchseqs + Console.traceln(Level.INFO, + "searching for patterns occuring most with " + nThreads + + " threads"); + // Prepare parallel search of matchseqs ExecutorService executor = Executors.newFixedThreadPool(nThreads); - int matchSeqSize=appData.getMatchseqs().size(); - int interval = Math.round(matchSeqSize/nThreads); + int matchSeqSize = appData.getMatchseqs().size(); + int interval = matchSeqSize / nThreads; int rest = matchSeqSize % nThreads; - - for(int i =0;i100) { - if((count%(size/100)==0)) { - //Console.traceln(Level.INFO,("Thread" + Thread.currentThread().getName() + ": " + Math.round((float) count/size*100))+ "%"); - System.out.println("Thread" + Thread.currentThread().getName() + ": " + Math.round((float) count/size*100)+ "%"); - } - } - else { - //Console.traceln(Level.INFO,("Thread" + Thread.currentThread().getName() + ": " +Math.round((float) count/size*100))+ "%"); - System.out.println("Thread" + Thread.currentThread().getName() + ": " +Math.round((float) count/size*100)+ "%"); - - } - } - - - - + + } + + // Print out the progress + private static void printProgressPercentage(int count, int size) { + if (size > 100) { + if ((count % (size / 100) == 0)) { + // Console.traceln(Level.INFO,("Thread" + + // Thread.currentThread().getName() + ": " + Math.round((float) + // count/size*100))+ "%"); + System.out.println("Thread" + Thread.currentThread().getName() + + ": " + Math.round((float) count / size * 100) + "%"); + } + } else { + // Console.traceln(Level.INFO,("Thread" + + // Thread.currentThread().getName() + ": " +Math.round((float) + // count/size*100))+ "%"); + System.out.println("Thread" + Thread.currentThread().getName() + + ": " + Math.round((float) count / size * 100) + "%"); + + } + } + + private class ParallelMatchReplacer implements Runnable { + + @Override + public void run() { + + } + + } + private class ParallelMatchOcurrencesFinder implements Runnable { - private final RuleApplicationData appData; - private final int from; - private final int to; - ParallelMatchOcurrencesFinder(RuleApplicationData appData, int from, int to) { - this.appData = appData; - this.from = from; - this.to = to; - } - - @Override - public void run() { - int count = 0; - int size=to-from; - - for (int i=from; i pattern - .getFirstSequence().size()) - continue; - - for (int j = 0; j < appData.getNumberSequences().size(); j++) { - LinkedList startpositions = appData - .getNumberSequences().get(j).containsPattern(pattern); - if (startpositions.size() > 0) { - for (Iterator jt = startpositions.iterator(); jt - .hasNext();) { - int start = jt.next(); - pattern.addOccurence(new MatchOccurence(start, start - + pattern.size(), j)); - } - } - } - } - } - } - - + private final RuleApplicationData appData; + private final int from; + private final int to; + + ParallelMatchOcurrencesFinder(RuleApplicationData appData, int from, + int to) { + this.appData = appData; + this.from = from; + this.to = to; + } + + @Override + public void run() { + int count = 0; + int size = to - from; + + for (int i = from; i < to; i++) { + Match pattern = appData.getMatchseqs().get(i); + count++; + printProgressPercentage(count, size); + // Skip sequences with more 0 events (scrolls) than other + // events. + // Both of the pattern sequences are equally long, so the zero + // counts just need to be smaller than the length of one + // sequence + if (pattern.getFirstSequence().eventCount(0) + + pattern.getSecondSequence().eventCount(0) + 1 > pattern + .getFirstSequence().size()) + continue; + + for (int j = 0; j < appData.getNumberSequences().size(); j++) { + LinkedList startpositions = appData + .getNumberSequences().get(j) + .containsPattern(pattern); + if (startpositions.size() > 0) { + for (Iterator jt = startpositions.iterator(); jt + .hasNext();) { + int start = jt.next(); + pattern.addOccurence(new MatchOccurence(start, + start + pattern.size(), j)); + } + } + } + } + } + } + private class ParallelPairwiseAligner implements Runnable { - private final RuleApplicationData appData; - private final int from; - private final int to; - ParallelPairwiseAligner(RuleApplicationData appData, int from, int to) { - this.appData = appData; - this.from = from; - this.to = to; - } - - @Override - public void run() { - int count = 0; - int size=to-from; - - for (int i=from; i generatePairwiseAlignments(RuleApplicationData appData) { + } + } + } + + // private LinkedList generatePairwiseAlignments(RuleApplicationData + // appData) { private void generatePairwiseAlignments(RuleApplicationData appData) { int numberSeqSize = appData.getNumberSequences().size(); appData.matchseqs = new LinkedList(); - //Checking if i have an already calculated file result of this action in the working directory - //File aligned = new File("aligned" + iteration + ".dat"); - //if(!(aligned.exists() && !aligned.isDirectory())) { - Console.traceln(Level.INFO, "generating pairwise alignments from " + numberSeqSize + " sessions with " + nThreads + " threads"); - ExecutorService executor = Executors.newFixedThreadPool(nThreads); - int interval = Math.round(numberSeqSize/nThreads); - int rest = numberSeqSize % nThreads; - - for (int i = 0; i < numberSeqSize-interval; i+=interval) { - int offset = 0; - if(rest!=0) { - offset=1; - rest--; - } - int from = i; - int to = i+interval+offset; - System.out.println("Creating thread for sessions " + from + " till " + to); - ParallelPairwiseAligner aligner = new ParallelPairwiseAligner(appData,from,to); - executor.execute(aligner); - } - executor.shutdown(); - try { - executor.awaitTermination(10, TimeUnit.MINUTES); - } catch (InterruptedException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - - //GlobalDataContainer.getInstance().addData("aligned" + iteration, appData); - //saveAppData("aligned" + iteration); - // return result; - } - //else { - // Console.traceln(Level.INFO,"loading matches from file"); - // appData = loadAppData("aligned"+iteration); - // return appData.getMatchseqs(); - //} - + Console.traceln(Level.INFO, "generating pairwise alignments from " + + numberSeqSize + " sessions with " + nThreads + " threads"); + ExecutorService executor = Executors.newFixedThreadPool(nThreads); + int interval = numberSeqSize / nThreads; + int rest = numberSeqSize % nThreads; + + for (int i = 0; i < numberSeqSize - interval; i += interval) { + int offset = 0; + if (rest != 0) { + offset = 1; + rest--; + } + int from = i; + int to = i + interval + offset; + System.out.println("Creating thread for sessions " + from + + " till " + to); + ParallelPairwiseAligner aligner = new ParallelPairwiseAligner( + appData, from, to); + executor.execute(aligner); + } + executor.shutdown(); + try { + executor.awaitTermination(2, TimeUnit.HOURS); + } catch (InterruptedException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + + } /** @@ -934,15 +948,18 @@ private HashMap number2task; - // TODO: We Actually just need number2task here, this structure can be removed in the future. + // TODO: We Actually just need number2task here, this structure can be + // removed in the future. private HashSet uniqueTasks; + + ObjectDistanceSubstitionMatrix submat; - ObjectDistanceSubstitionMatrix submat; + LinkedList matchseqs; - + private ArrayList numberseqs; private LinkedList newTasks; - + /** * @@ -975,5 +992,5 @@ stopWatch = new StopWatch(); result = new RuleApplicationResult(); - submat= new ObjectDistanceSubstitionMatrix(6,-3,false); + submat = new ObjectDistanceSubstitionMatrix(6, -3, false); newTasks = new LinkedList(); this.detectedAndReplacedTasks = true; @@ -984,14 +1001,13 @@ } - private ObjectDistanceSubstitionMatrix getSubmat() { return submat; } - + private void resetNewlyCreatedTasks() { uniqueTasks.addAll(newTasks); newTasks.clear(); } - + private void newTaskCreated(ITask task) { number2task.put(task.getId(), task); @@ -1023,6 +1039,4 @@ } - - /** * @@ -1042,5 +1056,5 @@ return newTasks; } - + /** * @return the stopWatch