Index: trunk/CrossPare/src/de/ugoe/cs/cpdp/loader/NetgeneFolderLoader.java
===================================================================
--- trunk/CrossPare/src/de/ugoe/cs/cpdp/loader/NetgeneFolderLoader.java (revision 124)
+++ trunk/CrossPare/src/de/ugoe/cs/cpdp/loader/NetgeneFolderLoader.java (revision 124)
@@ -0,0 +1,34 @@
+// Copyright 2016 Georg-August-Universität Göttingen, Germany
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package de.ugoe.cs.cpdp.loader;
+
+/**
+ * Implements the {@link AbstractFolderLoader} for the NETGENE data set.
+ *
+ * @author Steffen Herbold
+ */
+public class NetgeneFolderLoader extends AbstractFolderLoader {
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.ugoe.cs.cpdp.loader.AbstractFolderLoader#getSingleLoader()
+ */
+ @Override
+ protected SingleVersionLoader getSingleLoader() {
+ return new NetgeneLoader();
+ }
+
+}
Index: trunk/CrossPare/src/de/ugoe/cs/cpdp/loader/NetgeneLoader.java
===================================================================
--- trunk/CrossPare/src/de/ugoe/cs/cpdp/loader/NetgeneLoader.java (revision 124)
+++ trunk/CrossPare/src/de/ugoe/cs/cpdp/loader/NetgeneLoader.java (revision 124)
@@ -0,0 +1,198 @@
+// Copyright 2016 Georg-August-Universität Göttingen, Germany
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package de.ugoe.cs.cpdp.loader;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.logging.Level;
+
+import de.ugoe.cs.util.console.Console;
+import weka.core.Attribute;
+import weka.core.Instance;
+import weka.core.Instances;
+import weka.core.converters.CSVLoader;
+
+/**
+ *
+ * Loads the genealogy data published by Herzig et al.
+ *
+ *
+ * @author Steffen Herbold
+ */
+public class NetgeneLoader implements SingleVersionLoader {
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.ugoe.cs.cpdp.loader.SingleVersionLoader#load(java.io.File)
+ */
+ @Override
+ public Instances load(File fileMetricsFile) {
+ // first determine all files
+ String path = fileMetricsFile.getParentFile().getAbsolutePath();
+ String project = fileMetricsFile.getName().split("_")[0];
+ File bugsFile = new File(path + "/" + project + "_bugs_per_file.csv");
+ File networkMetrics = new File(path + "/" + project + "_network_metrics.csv");
+ Instances metricsData = null;
+
+ try {
+ CSVLoader wekaCsvLoader = new CSVLoader();
+ wekaCsvLoader.setSource(fileMetricsFile);
+ metricsData = wekaCsvLoader.getDataSet();
+ wekaCsvLoader.setSource(bugsFile);
+ Instances bugsData = wekaCsvLoader.getDataSet();
+ wekaCsvLoader.setSource(networkMetrics);
+ Instances networkData = wekaCsvLoader.getDataSet();
+
+ metricsData.setRelationName(project);
+
+ // fix nominal attributes (i.e., NA values)
+ for (int j = 2; j < networkData.numAttributes(); j++) {
+ if (networkData.attribute(j).isNominal()) {
+ String attributeName = networkData.attribute(j).name();
+ double[] tmpVals = new double[networkData.size()];
+ // get temporary values
+ for (int i = 0; i < networkData.size(); i++) {
+ Instance inst = networkData.instance(i);
+ if (!inst.isMissing(j)) {
+ String val = networkData.instance(i).stringValue(j);
+ try {
+ tmpVals[i] = Double.parseDouble(val);
+ }
+ catch (NumberFormatException e) {
+ // not a number, using 0.0;
+ tmpVals[i] = 0.0;
+ }
+ }
+ else {
+ tmpVals[i] = 0.0;
+ }
+ }
+ // replace attribute
+ networkData.deleteAttributeAt(j);
+ networkData.insertAttributeAt(new Attribute(attributeName), j);
+ for (int i = 0; i < networkData.size(); i++) {
+ networkData.instance(i).setValue(j, tmpVals[i]);
+ }
+ }
+ }
+ // fix string attributes
+ for (int j = 2; j < networkData.numAttributes(); j++) {
+ if (networkData.attribute(j).isString()) {
+ String attributeName = networkData.attribute(j).name();
+ double[] tmpVals = new double[networkData.size()];
+ // get temporary values
+ for (int i = 0; i < networkData.size(); i++) {
+ Instance inst = networkData.instance(i);
+ if (!inst.isMissing(j)) {
+ String val = networkData.instance(i).stringValue(j);
+ try {
+ tmpVals[i] = Double.parseDouble(val);
+ }
+ catch (NumberFormatException e) {
+ // not a number, using 0.0;
+ tmpVals[i] = 0.0;
+ }
+ }
+ else {
+ tmpVals[i] = 0.0;
+ }
+ }
+ // replace attribute
+ networkData.deleteAttributeAt(j);
+ networkData.insertAttributeAt(new Attribute(attributeName), j);
+ for (int i = 0; i < networkData.size(); i++) {
+ networkData.instance(i).setValue(j, tmpVals[i]);
+ }
+ }
+ }
+
+ Map filenames = new HashMap<>();
+ for (int j = 0; j < metricsData.size(); j++) {
+ filenames.put(metricsData.instance(j).stringValue(0), j);
+ }
+ // merge with network data
+ int attributeIndex;
+ for (int j = 2; j < networkData.numAttributes(); j++) {
+ attributeIndex = metricsData.numAttributes();
+ metricsData.insertAttributeAt(networkData.attribute(j), attributeIndex);
+ for (int i = 0; i < networkData.size(); i++) {
+ Integer instanceIndex = filenames.get(networkData.instance(i).stringValue(1));
+ if (instanceIndex != null) {
+ metricsData.instance(instanceIndex)
+ .setValue(attributeIndex, networkData.instance(i).value(j));
+ }
+ }
+ }
+
+ // add bug information
+ attributeIndex = metricsData.numAttributes();
+ final ArrayList classAttVals = new ArrayList();
+ classAttVals.add("0");
+ classAttVals.add("1");
+ final Attribute classAtt = new Attribute("bug", classAttVals);
+ metricsData.insertAttributeAt(classAtt, attributeIndex);
+ for (int i = 0; i < bugsData.size(); i++) {
+ if (bugsData.instance(i).value(2) > 0.0d) {
+ Integer instanceIndex = filenames.get(bugsData.instance(i).stringValue(1));
+ if (instanceIndex != null) {
+ metricsData.instance(instanceIndex).setValue(attributeIndex, 1.0);
+ }
+ }
+ }
+
+ // remove filenames
+ metricsData.deleteAttributeAt(0);
+ Attribute eigenvector = metricsData.attribute("eigenvector");
+ if (eigenvector != null) {
+ for (int j = 0; j < metricsData.numAttributes(); j++) {
+ if (metricsData.attribute(j) == eigenvector) {
+ metricsData.deleteAttributeAt(j);
+ }
+ }
+ }
+
+ metricsData.setClassIndex(metricsData.numAttributes() - 1);
+
+ // set all missing values to 0
+ for (int i = 0; i < metricsData.size(); i++) {
+ for (int j = 0; j < metricsData.numAttributes(); j++) {
+ if (metricsData.instance(i).isMissing(j)) {
+ metricsData.instance(i).setValue(j, 0.0d);
+ }
+ }
+ }
+ }
+ catch (IOException e) {
+ Console.traceln(Level.SEVERE, "failure reading file: " + e.getMessage());
+ metricsData = null;
+ }
+ return metricsData;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see de.ugoe.cs.cpdp.loader.SingleVersionLoader#filenameFilter(java.lang.String)
+ */
+ @Override
+ public boolean filenameFilter(String filename) {
+ return filename.endsWith("fileMetrics.csv");
+ }
+
+}