Refactored code:

renamed Instance's getContinuous(int) method to get(int), since all it was doing was getting the ith element (not getting the ith continuous element as claimed) removed a few extraneous imports
jenleong · Oct 18, 2014 · 28c9919 · 28c9919
1 parent 45b6a52
commit 28c9919
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Showing 24 changed files with 72 additions and 51 deletions.
diff --git a/src/dist/PrecalculatedDistribution.java b/src/dist/PrecalculatedDistribution.java
@@ -42,7 +42,7 @@ public Instance mode(Instance input) {
      * @see hmm.distribution.OutputDistribution#probabilityOfObservation(hmm.observation.Observation)
      */
     public double p(Instance inst) {
-        return inst.getContinuous(i);
+        return inst.get(i);
     }
 
 

diff --git a/src/func/inst/HyperRectangle.java b/src/func/inst/HyperRectangle.java
@@ -108,12 +108,12 @@ public HyperRectangle splitRight(double value, int dimension) {
     public Instance pointNearestTo(Instance target) {
         double[] nearest = new double[target.size()];
         for (int i = 0; i < nearest.length; i++) {
-            if (target.getContinuous(i) <= min.get(i)) {
+            if (target.get(i) <= min.get(i)) {
                 nearest[i] = min.get(i);
-            } else if (target.getContinuous(i) >= max.get(i)) {
+            } else if (target.get(i) >= max.get(i)) {
                 nearest[i] = max.get(i);
             } else {
-                nearest[i] = target.getContinuous(i);
+                nearest[i] = target.get(i);
             }
         }
         return new Instance(new DenseVector(nearest));

diff --git a/src/func/inst/KDTree.java b/src/func/inst/KDTree.java
@@ -156,8 +156,8 @@ private int chooseSplitterSmart(KDTreeNode[] nodes, int start, int end) {
         for (int i = start; i < end; i++) {
             Instance key = nodes[i].getInstance();
             for (int j = 0; j < dimensions; j++) {
-                min[j] = Math.min(min[j], key.getContinuous(j));
-                max[j] = Math.max(max[j], key.getContinuous(j));
+                min[j] = Math.min(min[j], key.get(j));
+                max[j] = Math.max(max[j], key.get(j));
             }
         }
         // find the widest dimension
@@ -176,11 +176,11 @@ private int chooseSplitterSmart(KDTreeNode[] nodes, int start, int end) {
         int splitterIndex = -1; 
         for (int i = start; i < end; i++) {
             KDTreeNode node = nodes[i];
-            if (Math.abs(node.getInstance().getContinuous(widestDimension) - median)
+            if (Math.abs(node.getInstance().get(widestDimension) - median)
                 < bestDifference) {
                 splitterIndex = i;
                 bestDifference =
-                    Math.abs(node.getInstance().getContinuous(widestDimension) - median);
+                    Math.abs(node.getInstance().get(widestDimension) - median);
             }
         }
         nodes[splitterIndex].setDimension(widestDimension);
@@ -253,7 +253,7 @@ private void knn(KDTreeNode node, Instance target, HyperRectangle hr,
             node.getSplitValue(), node.getDimension());
         HyperRectangle nearHR, farHR;
         KDTreeNode nearNode, farNode;
-        if (target.getContinuous(node.getDimension()) < node.getSplitValue()) {
+        if (target.get(node.getDimension()) < node.getSplitValue()) {
             nearHR = leftHR; nearNode = node.getLeft();
             farHR = rightHR; farNode = node.getRight();
         } else {

diff --git a/src/func/inst/KDTreeNode.java b/src/func/inst/KDTreeNode.java
@@ -41,7 +41,7 @@ public KDTreeNode(Instance key) {
      * @return the value
      */
     public double getSplitValue() {
-        return instance.getContinuous(dimension);
+        return instance.get(dimension);
     }
 
     /**
@@ -105,7 +105,7 @@ public void setRight(KDTreeNode node) {
      */
     public int compareTo(Object o) {
         double value = getSplitValue();
-        double otherValue = ((KDTreeNode) o).getInstance().getContinuous(dimension);
+        double otherValue = ((KDTreeNode) o).getInstance().get(dimension);
         if (value < otherValue) {
             return -1;
         } else if (value > otherValue) {

diff --git a/src/opt/ContinuousAddOneNeighbor.java b/src/opt/ContinuousAddOneNeighbor.java
@@ -36,7 +36,7 @@ public ContinuousAddOneNeighbor() {
     public Instance neighbor(Instance d) {
         int i = Distribution.random.nextInt(d.size());
         Instance cod = (Instance) d.copy();
-        cod.getData().set(i, cod.getContinuous(i)+ Distribution.random.nextDouble() * amount - amount / 2);
+        cod.getData().set(i, cod.get(i)+ Distribution.random.nextDouble() * amount - amount / 2);
         return cod;
     }
 }
diff --git a/src/opt/SwapNeighbor.java b/src/opt/SwapNeighbor.java
@@ -18,8 +18,8 @@ public Instance neighbor(Instance d) {
         Instance cod = (Instance) d.copy();
         int i = Distribution.random.nextInt(cod.getData().size());
         int j = Distribution.random.nextInt(cod.getData().size());
-        double temp = cod.getContinuous(i);
-        cod.getData().set(i, cod.getContinuous(j));
+        double temp = cod.get(i);
+        cod.getData().set(i, cod.get(j));
         cod.getData().set(j, temp);
         return cod;
     }

diff --git a/src/opt/example/TravelingSalesmanSortEvaluationFunction.java b/src/opt/example/TravelingSalesmanSortEvaluationFunction.java
@@ -26,7 +26,7 @@ public TravelingSalesmanSortEvaluationFunction(double[][] points) {
     public double value(Instance d) {
         double[] ddata = new double[d.size()];
         for (int i = 0; i < ddata.length; i++) {
-            ddata[i] = d.getContinuous(i);
+            ddata[i] = d.get(i);
         }
         int[] order = ABAGAILArrays.indices(d.size());
         ABAGAILArrays.quicksort(ddata, order);

diff --git a/src/opt/ga/ContinuousAddOneMutation.java b/src/opt/ga/ContinuousAddOneMutation.java
@@ -35,6 +35,6 @@ public ContinuousAddOneMutation() {
      */
     public void mutate(Instance cod) {
         int i = Distribution.random.nextInt(cod.size());
-        cod.getData().set(i, cod.getContinuous(i)+ Distribution.random.nextDouble() * amount - amount / 2);
+        cod.getData().set(i, cod.get(i)+ Distribution.random.nextDouble() * amount - amount / 2);
     }
 }
diff --git a/src/opt/ga/SingleCrossOver.java b/src/opt/ga/SingleCrossOver.java
@@ -19,9 +19,9 @@ public Instance mate(Instance a, Instance b) {
         int point = Distribution.random.nextInt(newData.length + 1);
         for (int i = 0; i < newData.length; i++) {
             if (i >= point) {
-                newData[i] = a.getContinuous(i);
+                newData[i] = a.get(i);
             } else {
-                newData[i] = b.getContinuous(i);
+                newData[i] = b.get(i);
             }
         }
         return new Instance(newData);

diff --git a/src/opt/ga/SwapMutation.java b/src/opt/ga/SwapMutation.java
@@ -16,8 +16,8 @@ public class SwapMutation implements MutationFunction {
     public void mutate(Instance d) {
         int i = Distribution.random.nextInt(d.size());
         int j = Distribution.random.nextInt(d.size());
-        double temp = d.getContinuous(i);
-        d.getData().set(i, d.getContinuous(j));
+        double temp = d.get(i);
+        d.getData().set(i, d.get(j));
         d.getData().set(j, temp);
     }
 }
diff --git a/src/opt/ga/UniformCrossOver.java b/src/opt/ga/UniformCrossOver.java
@@ -18,9 +18,9 @@ public Instance mate(Instance a, Instance b) {
         double[] newData = new double[a.size()];
         for (int i = 0; i < newData.length; i++) {
             if (Distribution.random.nextBoolean()) {
-                newData[i] = a.getContinuous(i);
+                newData[i] = a.get(i);
             } else {
-                newData[i] = b.getContinuous(i);
+                newData[i] = b.get(i);
             }
         }
         return new Instance(newData);

diff --git a/src/shared/DataSetDescription.java b/src/shared/DataSetDescription.java
@@ -271,12 +271,12 @@ public void induceFrom(DataSet data) {
             min.minEquals(cur.getData());
             for (int j = 0; j < types.length; j++) {
                 if (types[j] == AttributeType.BINARY
-                        && cur.getContinuous(j) != 1 && cur.getContinuous(j) != 0) {
+                        && cur.get(j) != 1 && cur.get(j) != 0) {
 
                     types[j] = AttributeType.DISCRETE;
                 }
                 if (types[j] == AttributeType.DISCRETE
-                        && cur.getDiscrete(j) != cur.getContinuous(j)) {
+                        && cur.getDiscrete(j) != cur.get(j)) {
                     types[j] = AttributeType.CONTINUOUS;      
                 }
             }

diff --git a/src/shared/DataSetWriter.java b/src/shared/DataSetWriter.java
@@ -84,7 +84,7 @@ public void write() throws IOException {
                     }
                 } else {
                     for (int j = 0; j < data.size(); j++) {
-                        pw.print(data.getContinuous(j));
+                        pw.print(data.get(j));
                         if (j + 1 < data.size() || data.getLabel() != null) {
                             pw.print(", ");
                         }

diff --git a/src/shared/EuclideanDistance.java b/src/shared/EuclideanDistance.java
@@ -14,8 +14,8 @@ public class EuclideanDistance extends AbstractDistanceMeasure {
     public double value(Instance va, Instance vb) {
         double sum = 0;
         for (int i = 0; i < va.size(); i++) {
-            sum += (va.getContinuous(i) - vb.getContinuous(i)) 
-                 * (va.getContinuous(i) - vb.getContinuous(i));
+            sum += (va.get(i) - vb.get(i))
+                 * (va.get(i) - vb.get(i));
         }
         return sum;
     }

diff --git a/src/shared/Instance.java b/src/shared/Instance.java
@@ -137,11 +137,11 @@ public int size() {
     }
 
     /**
-     * Get the ith continuous value
-     * @param i the value to get
+     * Get the ith value
+     * @param i the index of the value to get
      * @return the value
      */
-    public double getContinuous(int i) {
+    public double get(int i) {
         return data.get(i);
     }
 
@@ -159,7 +159,7 @@ public int getDiscrete(int i) {
      * @return the value
      */
     public double getContinuous() {
-        return getContinuous(0);
+        return get(0);
     }
 
     /**

diff --git a/src/shared/MixedDistanceMeasure.java b/src/shared/MixedDistanceMeasure.java
@@ -29,8 +29,8 @@ public double value(Instance va, Instance vb) {
         double distance = 0;
         for (int i = 0; i < va.size(); i++) {
             if (types[i] == AttributeType.CONTINUOUS) {
-                distance += (va.getContinuous(i) - vb.getContinuous(i)) 
-                     * (va.getContinuous(i) - vb.getContinuous(i));
+                distance += (va.get(i) - vb.get(i))
+                     * (va.get(i) - vb.get(i));
             } else {
                 if (va.getDiscrete(i) != vb.getDiscrete(i)) {
                     distance += 1;

diff --git a/src/shared/SumOfSquaresError.java b/src/shared/SumOfSquaresError.java
@@ -20,8 +20,8 @@ public double value(Instance output, Instance example) {
         double sum = 0;
         Instance label = example.getLabel();
         for (int i = 0; i < output.size(); i++) {
-            sum += (output.getContinuous(i) - label.getContinuous(i)) 
-                * (output.getContinuous(i) - label.getContinuous(i))
+            sum += (output.get(i) - label.get(i))
+                * (output.get(i) - label.get(i))
                 * example.getWeight();
         }
         return .5 * sum;
@@ -34,7 +34,7 @@ public double[] gradient(Instance output, Instance example) {
         double[] errorArray = new double[output.size()];
         Instance label = example.getLabel();
         for (int i = 0; i < output.size(); i++) {
-            errorArray[i] = (output.getContinuous(i) - label.getContinuous(i))
+            errorArray[i] = (output.get(i) - label.get(i))
                 * example.getWeight();
         }
         return errorArray;

diff --git a/src/shared/filt/ContinuousToDiscreteFilter.java b/src/shared/filt/ContinuousToDiscreteFilter.java
@@ -37,16 +37,16 @@ public void filter(DataSet dataSet) {
             Instance instance = dataSet.get(i);
             for (int j = 0; j < oldDescription.getAttributeCount(); j++) {
                 if (oldDescription.getAttributeTypes()[j] == AttributeType.CONTINUOUS) {
-                    double cv = instance.getContinuous(j);
+                    double cv = instance.get(j);
                     int dv = (int) ((cv - oldDescription.getMin(j)) 
                         * numberOfBins / oldDescription.getRange(j));
                     instance.getData().set(j, dv);
                 }
             }
         }
-
-        // the description is no longer valid so generate a new one
-        dataSet.setDescription(new DataSetDescription(dataSet));
-        dataSet.getDescription().setLabelDescription(new DataSetDescription(dataSet.getLabelDataSet()));
+
+        // the description is no longer valid so generate a new one
+        dataSet.setDescription(new DataSetDescription(dataSet));
+        dataSet.getDescription().setLabelDescription(new DataSetDescription(dataSet.getLabelDataSet()));
     }
 }
diff --git a/src/shared/filt/DiscreteToBinaryFilter.java b/src/shared/filt/DiscreteToBinaryFilter.java
@@ -43,7 +43,7 @@ public void filter(DataSet dataSet) {
                     data[k + instance.getDiscrete(j)] = 1;
                     k += oldDescription.getDiscreteRange(j);
                 } else {
-                    data[k] = instance.getContinuous(j);
+                    data[k] = instance.get(j);
                     k++;
                 }
             }

diff --git a/src/shared/reader/DataSetLabelBinarySeperator.java b/src/shared/reader/DataSetLabelBinarySeperator.java
@@ -5,7 +5,6 @@
 
 import shared.DataSet;
 import shared.Instance;
-import shared.tester.Comparison;
 
 /**
  * Separates Discrete Labels into Binary representation for better use in Neural Networks
@@ -61,7 +60,7 @@ public static Instance combineLabels(Instance instance) {
         int maxInx = -1;
         double max = 0;
         for (int ii = 0; ii < instance.size(); ii++) {
-            double inst = instance.getContinuous(ii);
+            double inst = instance.get(ii);
             if (inst > max) {
                 maxInx = ii;
                 max    = inst;

diff --git a/src/shared/runner/Experiment.java b/src/shared/runner/Experiment.java
@@ -0,0 +1,24 @@
+package shared.runner;
+
+import shared.DataSet;
+import shared.reader.DataSetReader;
+
+/**
+ * Created by zooky on 10/11/14.
+ */
+public interface Experiment {
+    /**
+     * Set type of DataSetReader according to type of datafile
+     */
+    public void setDataSetReader();
+    /**
+     *
+     * @return A DataSet
+     */
+    public DataSet getDataSet();
+
+
+
+
+
+}
diff --git a/src/shared/tester/Comparison.java b/src/shared/tester/Comparison.java
@@ -1,7 +1,6 @@
 package shared.tester;
 
 import shared.Instance;
-import util.linalg.Vector;
 
 /**
  * An generic utility for comparing values in Instance objects
@@ -55,7 +54,7 @@ public boolean isAllCorrect() {
     public boolean isCorrect(int index) {
         //compare the continuous values, down to 1e-6.  This accounts for any weird floating point issues, and some
         // issues when classifying discrete or boolean functions.
-        return Math.abs(expected.getContinuous(index) - actual.getContinuous(index)) < epsilon;
+        return Math.abs(expected.get(index) - actual.get(index)) < epsilon;
     }
 
     /**

diff --git a/src/shared/tester/ConfusionMatrixTestMetric.java b/src/shared/tester/ConfusionMatrixTestMetric.java
@@ -6,7 +6,6 @@
 import shared.AttributeType;
 import shared.DataSetDescription;
 import shared.Instance;
-import shared.reader.DataSetLabelBinarySeperator;
 
 /**
  * A test metric to generate a confusion matrix.  This metric expects the true labels
@@ -57,8 +56,8 @@ public int hashCode() {
             for (int ii = 0; ii < expected.size(); ii++) {
                 //scale the expected value, to provide separation between corresponding pairs
                 // (e.g. a, b should be different from b, a)
-                hashCode += 0x10000 * expected.getContinuous(ii);
-                hashCode += actual.getContinuous(ii);
+                hashCode += 0x10000 * expected.get(ii);
+                hashCode += actual.get(ii);
             }
             return hashCode;
         }

diff --git a/src/shared/tester/RawOutputTestMetric.java b/src/shared/tester/RawOutputTestMetric.java
@@ -13,7 +13,7 @@ public void addResult(Instance expected, Instance actual) {
             if (addComma) {
                 builder.append(",");
             }
-            builder.append(expected.getContinuous(ii));
+            builder.append(expected.get(ii));
             addComma = true;
         }
         builder.append(", Actual: ");
@@ -22,7 +22,7 @@ public void addResult(Instance expected, Instance actual) {
             if (addComma) {
                 builder.append(",");
             }
-            builder.append(actual.getContinuous(ii));
+            builder.append(actual.get(ii));
             addComma = true;
         }