Changeset 1718 for branches/autoquest-core-tasktrees-alignment/src

Timestamp:

09/03/14 10:13:25 (10 years ago)

Author:

rkrimmel

Message:

Saving everything to file.

File:

• branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (11 diffs)

branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

@@ -15 +15 @@
 package de.ugoe.cs.autoquest.tasktrees.temporalrelation;
 
+import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
@@ -77 +78 @@
         
         
-        public static int nThreads;
-        public static boolean harmonizeSequences;
-        public static boolean loadSubstutionMatrix;
-        
 
         private int iteration = 0;
@@ -193 +190 @@
         public RuleApplicationResult apply(List<IUserSession> sessions) {
                 RuleApplicationData appData = new RuleApplicationData(sessions);
-                if(SequenceForTaskDetectionRuleAlignment.harmonizeSequences) {
+                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);
@@ -202 +204 @@
                         saveAppData("harmonized");
                 }
-                else {
-                        Console.traceln(Level.INFO,"loading harmonized sessions from file");
-                        appData = loadAppData("harmonized");
-                }
-                System.out.println(SequenceForTaskDetectionRuleAlignment.loadSubstutionMatrix);
-                if(!SequenceForTaskDetectionRuleAlignment.loadSubstutionMatrix) {       
+                
+                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");
@@ -651 +650 @@
                 // Generate pairwise alignments
                 int size = appData.getNumberSequences().size();
-                Console.traceln(Level.INFO, "generating pairwise alignments");
-                LinkedList<Match> matchseqs = new LinkedList<Match>();
+                Console.traceln(Level.INFO, "generating pairwise alignments from " + size + " sessions");
                 int count = 0;
                 
-                for (int i = 0; i < appData.getNumberSequences().size(); i++) {
-                        NumberSequence ns1 = appData.getNumberSequences().get(i);
-                        count++;
-        //              if((count%(size/100)==0)) {
-        //                      Console.traceln(Level.INFO,(Math.round((float) count/size*100))+ "%");
-        //              }
-                        for (int j = 0; j < appData.getNumberSequences().size(); j++) {
-                                NumberSequence ns2 = appData.getNumberSequences().get(j);
-                                if (i != j) {
-                                        //Console.traceln(Level.FINEST,"Aligning sequence " + i + " with sequence " + j);
-                                        AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
-                                        aa.align(ns1, ns2, appData.getSubmat(),9);
-                                        matchseqs.addAll(aa.getMatches());
-                                }
-                        }
-                }
-                GlobalDataContainer.getInstance().addData("aligned", matchseqs);
-                saveAppData("aligned");
+                //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())) {
+                        appData.matchseqs = new LinkedList<Match>();
+                        System.out.println(appData.matchseqs);
+                        for (int i = 0; i < appData.getNumberSequences().size(); i++) {
+                                NumberSequence ns1 = appData.getNumberSequences().get(i);
+                                count++;
+                                
+                                //Print out the progress
+                                if(size>100) {
+                                        if((count%(size/100)==0)) {     
+                                                Console.traceln(Level.INFO,(Math.round((float) count/size*100))+ "%");
+                                        }
+                                }
+                                else {
+                                        Console.traceln(Level.INFO,(Math.round((float) count/size*100))+ "%");
+                                }
+                                for (int j = 0; j < appData.getNumberSequences().size(); j++) {
+                                        NumberSequence ns2 = appData.getNumberSequences().get(j);
+                                        if (i != j) {
+                                                //Console.traceln(Level.FINEST,"Aligning sequence " + i + " with sequence " + j);
+                                                AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create();
+                                                aa.align(ns1, ns2, appData.getSubmat(),9);
+                                                appData.getMatchseqs().addAll(aa.getMatches());
+                                        }
+                                }
+                        }
+                        GlobalDataContainer.getInstance().addData("aligned" + iteration, appData);
+                        saveAppData("aligned" + iteration);
+                }
+                else {
+                        Console.traceln(Level.INFO,"loading matches from file");
+                        appData = loadAppData("aligned"+iteration);
+                }
+
 
                 Console.traceln(Level.INFO, "searching for patterns occuring most");
 
                 // search each match in every other sequence
-                for (Iterator<Match> it = matchseqs.iterator(); it.hasNext();) {
+                for (Iterator<Match> it = appData.getMatchseqs().iterator(); it.hasNext();) {
                         Match pattern = it.next();
-
+                        
                         // Skip sequences with more 0 events (scrolls) than other events.
                         // Both of the pattern sequences are equally long, so the zero
@@ -711 +727 @@
                         }
                 };
-                Collections.sort(matchseqs, comparator);
+                Collections.sort(appData.getMatchseqs(), comparator);
                 appData.getStopWatch().stop("detecting tasks");
 
@@ -717 +733 @@
                 HashMap<Integer, List<MatchOccurence>> replacedOccurences = new HashMap<Integer, List<MatchOccurence>>();
                 // Replace matches in the sessions
-                for (int i = 0; i < matchseqs.size(); i++) {
+                for (int i = 0; i < appData.getMatchseqs().size(); i++) {
+                
                         // Every pattern consists of 2 sequences, therefore the minimum
                         // occurrences here is 2.
                         // We just need the sequences also occurring in other sequences as
                         // well
-                        if (matchseqs.get(i).occurenceCount() > 2) {
-
+                        if (appData.getMatchseqs().get(i).occurenceCount() > 2) {
                                 appData.detectedAndReplacedTasks = true;
-                                ISequence task = matchAsSequence(appData, matchseqs.get(i));
-                                invalidOccurence: for (Iterator<MatchOccurence> it = matchseqs
+                                ISequence task = matchAsSequence(appData, appData.getMatchseqs().get(i));
+                                invalidOccurence: for (Iterator<MatchOccurence> it = appData.getMatchseqs()
                                                 .get(i).getOccurences().iterator(); it.hasNext();) {
                                         MatchOccurence oc = it.next();
                                         
                                         /*
-                                        if (iteration > 1) {
+                                        if (iteration > 0) {
                                          
                                         System.out.println("Trying to replace sequence: ");
-                                        matchseqs.get(i).getFirstSequence().printSequence();
-                                        matchseqs.get(i).getSecondSequence().printSequence();
+                                        appData.getMatchseqs().get(i).getFirstSequence().printSequence();
+                                        appData.getMatchseqs().get(i).getSecondSequence().printSequence();
                                         System.out.println(" in session number: "
                                                         + (oc.getSequenceId() + 1) + " at position "
@@ -808 +824 @@
                         }
                 }
-                matchseqs = null;
+                appData.setMatchseqs(null);
                 appData.getStopWatch().stop("replacing tasks");
         }
@@ -828 +844 @@
                 
                 ObjectDistanceSubstitionMatrix submat; 
-
-        
+                
+                LinkedList<Match> matchseqs;
+                
                 private ArrayList<NumberSequence> numberseqs;
 
@@ -868 +885 @@
                 }
 
+                public LinkedList<Match> getMatchseqs() {
+                        return matchseqs;
+                }
+
+                public void setMatchseqs(LinkedList<Match> matchseqs) {
+                        this.matchseqs = matchseqs;
+                }
+
                 private ObjectDistanceSubstitionMatrix getSubmat() {
                         return submat;
@@ -907 +932 @@
 
                 
+                
                 /**
          *