/* * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. */ /* * Copyright (C) 2006 University of Waikato */ package weka.attributeSelection; import weka.core.Attribute; import weka.core.CheckGOE; import weka.core.CheckOptionHandler; import weka.core.Instances; import weka.core.CheckScheme.PostProcessor; import weka.test.Regression; import junit.framework.TestCase; /** * Abstract Test class for attribute selection schemes. Internally it uses the * class CheckAttributeSelection to determine success or failure * of the tests. It follows basically the testsPerClassType * method. * * @author FracPete (fracpete at waikato dot ac dot nz) * @version $Revision: 1.5 $ * * @see CheckAttributeSelection * @see CheckAttributeSelection#testsPerClassType(int, boolean, boolean) * @see PostProcessor */ public abstract class AbstractAttributeSelectionTest extends TestCase { /** The search scheme to be tested */ protected ASSearch m_Search; /** The evaluator to test */ protected ASEvaluation m_Evaluator; /** For testing the attribute selection scheme */ protected CheckAttributeSelection m_Tester; /** whether scheme handles weighted instances */ protected boolean m_weightedInstancesHandler; /** whether scheme handles multi-instance data */ protected boolean m_multiInstanceHandler; /** the number of classes to test with testNClasses() * @see #testNClasses() */ protected int m_NClasses; /** whether to run CheckAttributeSelection in DEBUG mode */ protected boolean DEBUG = false; /** the attribute type with the lowest value */ protected final static int FIRST_CLASSTYPE = Attribute.NUMERIC; /** the attribute type with the highest value */ protected final static int LAST_CLASSTYPE = Attribute.RELATIONAL; /** wether scheme can predict nominal attributes (array index is attribute type of class) */ protected boolean[] m_NominalPredictors; /** wether scheme can predict numeric attributes (array index is attribute type of class) */ protected boolean[] m_NumericPredictors; /** wether scheme can predict string attributes (array index is attribute type of class) */ protected boolean[] m_StringPredictors; /** wether scheme can predict date attributes (array index is attribute type of class) */ protected boolean[] m_DatePredictors; /** wether scheme can predict relational attributes (array index is attribute type of class) */ protected boolean[] m_RelationalPredictors; /** whether scheme handles missing values */ protected boolean[] m_handleMissingPredictors; /** whether scheme handles class with only missing values */ protected boolean[] m_handleMissingClass; /** whether scheme handles class as first attribute */ protected boolean[] m_handleClassAsFirstAttribute; /** whether scheme handles class as second attribute */ protected boolean[] m_handleClassAsSecondAttribute; /** the results of the regression tests */ protected String[] m_RegressionResults; /** the OptionHandler tester */ protected CheckOptionHandler m_OptionTester; /** for testing GOE stuff */ protected CheckGOE m_GOETester; /** * Constructs the AbstractAttributeSelectionTest. Called by subclasses. * * @param name the name of the test class */ public AbstractAttributeSelectionTest(String name) { super(name); } /** * returns a custom PostProcessor for the CheckAttributeSelection datasets, * currently only null. * * @return a custom PostProcessor, if necessary * @see PostProcessor */ protected PostProcessor getPostProcessor() { return null; } /** * configures the CheckAttributeSelection instance used throughout the tests * * @return the fully configured CheckAttributeSelection instance used for testing */ protected CheckAttributeSelection getTester() { CheckAttributeSelection result; result = new CheckAttributeSelection(); result.setSilent(true); result.setSearch(m_Search); result.setEvaluator(m_Evaluator); result.setNumInstances(20); result.setDebug(DEBUG); result.setPostProcessor(getPostProcessor()); return result; } /** * Configures the CheckOptionHandler uses for testing the optionhandling. * Sets the scheme to test. * * @return the fully configured CheckOptionHandler */ protected CheckOptionHandler getOptionTester() { CheckOptionHandler result; result = new CheckOptionHandler(); result.setOptionHandler(null); result.setUserOptions(new String[0]); result.setSilent(true); return result; } /** * Configures the CheckGOE used for testing GOE stuff. * * @return the fully configured CheckGOE */ protected CheckGOE getGOETester() { CheckGOE result; result = new CheckGOE(); result.setObject(null); result.setSilent(true); return result; } /** * Called by JUnit before each test method. This implementation creates * the default scheme to test and loads a test set of Instances. * * @exception Exception if an error occurs reading the example instances. */ protected void setUp() throws Exception { m_Search = getSearch(); m_Evaluator = getEvaluator(); m_Tester = getTester(); m_OptionTester = getOptionTester(); m_GOETester = getGOETester(); m_weightedInstancesHandler = m_Tester.weightedInstancesHandler()[0]; m_multiInstanceHandler = m_Tester.multiInstanceHandler()[0]; m_NominalPredictors = new boolean[LAST_CLASSTYPE + 1]; m_NumericPredictors = new boolean[LAST_CLASSTYPE + 1]; m_StringPredictors = new boolean[LAST_CLASSTYPE + 1]; m_DatePredictors = new boolean[LAST_CLASSTYPE + 1]; m_RelationalPredictors = new boolean[LAST_CLASSTYPE + 1]; m_handleMissingPredictors = new boolean[LAST_CLASSTYPE + 1]; m_handleMissingClass = new boolean[LAST_CLASSTYPE + 1]; m_handleClassAsFirstAttribute = new boolean[LAST_CLASSTYPE + 1]; m_handleClassAsSecondAttribute = new boolean[LAST_CLASSTYPE + 1]; m_RegressionResults = new String[LAST_CLASSTYPE + 1]; m_NClasses = 4; // initialize attributes checkAttributes(true, false, false, false, false, false); checkAttributes(false, true, false, false, false, false); checkAttributes(false, false, true, false, false, false); checkAttributes(false, false, false, true, false, false); checkAttributes(false, false, false, false, true, false); // initialize missing values handling for (int i = FIRST_CLASSTYPE; i <= LAST_CLASSTYPE; i++) { // does the scheme support this type of class at all? if (!canPredict(i)) continue; // 20% missing m_handleMissingPredictors[i] = checkMissingPredictors(i, 20, false); m_handleMissingClass[i] = checkMissingClass(i, 20, false); } } /** Called by JUnit after each test method */ protected void tearDown() { m_Search = null; m_Evaluator = null; m_Tester = null; m_OptionTester = null; m_GOETester = null; m_weightedInstancesHandler = false; m_NominalPredictors = new boolean[LAST_CLASSTYPE + 1]; m_NumericPredictors = new boolean[LAST_CLASSTYPE + 1]; m_StringPredictors = new boolean[LAST_CLASSTYPE + 1]; m_DatePredictors = new boolean[LAST_CLASSTYPE + 1]; m_RelationalPredictors = new boolean[LAST_CLASSTYPE + 1]; m_handleMissingPredictors = new boolean[LAST_CLASSTYPE + 1]; m_handleMissingClass = new boolean[LAST_CLASSTYPE + 1]; m_handleClassAsFirstAttribute = new boolean[LAST_CLASSTYPE + 1]; m_handleClassAsSecondAttribute = new boolean[LAST_CLASSTYPE + 1]; m_RegressionResults = new String[LAST_CLASSTYPE + 1]; m_NClasses = 4; } /** * Used to create an instance of a specific search scheme. * * @return a suitably configured ASSearch value */ public abstract ASSearch getSearch(); /** * Used to create an instance of a specific evaluator. * * @return a suitably configured ASEvaluation value */ public abstract ASEvaluation getEvaluator(); /** * checks whether at least one attribute type can be handled with the * given class type * * @param type the class type to check for * @return true if at least one attribute type can be predicted with * the given class */ protected boolean canPredict(int type) { return m_NominalPredictors[type] || m_NumericPredictors[type] || m_StringPredictors[type] || m_DatePredictors[type] || m_RelationalPredictors[type]; } /** * returns a string for the class type * * @param type the class type * @return the class type as string */ protected String getClassTypeString(int type) { return CheckAttributeSelection.attributeTypeToString(type); } /** * tests whether the scheme can handle certain attributes and if not, * if the exception is OK * * @param nom to check for nominal attributes * @param num to check for numeric attributes * @param str to check for string attributes * @param dat to check for date attributes * @param rel to check for relational attributes * @param allowFail whether a junit fail can be executed * @see CheckAttributeSelection#canPredict(boolean, boolean, boolean, boolean, boolean, boolean, int) * @see CheckAttributeSelection#testsPerClassType(int, boolean, boolean) */ protected void checkAttributes(boolean nom, boolean num, boolean str, boolean dat, boolean rel, boolean allowFail) { boolean[] result; String att; int i; // determine text for type of attributes att = ""; if (nom) att = "nominal"; else if (num) att = "numeric"; else if (str) att = "string"; else if (dat) att = "date"; else if (rel) att = "relational"; for (i = FIRST_CLASSTYPE; i <= LAST_CLASSTYPE; i++) { result = m_Tester.canPredict(nom, num, str, dat, rel, m_multiInstanceHandler, i); if (nom) m_NominalPredictors[i] = result[0]; else if (num) m_NumericPredictors[i] = result[0]; else if (str) m_StringPredictors[i] = result[0]; else if (dat) m_DatePredictors[i] = result[0]; else if (rel) m_RelationalPredictors[i] = result[0]; if (!result[0] && !result[1] && allowFail) fail("Error handling " + att + " attributes (" + getClassTypeString(i) + " class)!"); } } /** * tests whether the scheme can handle different types of attributes and * if not, if the exception is OK * * @see #checkAttributes(boolean, boolean, boolean, boolean, boolean, boolean) */ public void testAttributes() { // nominal checkAttributes(true, false, false, false, false, true); // numeric checkAttributes(false, true, false, false, false, true); // string checkAttributes(false, false, true, false, false, true); // date checkAttributes(false, false, false, true, false, true); // relational if (!m_multiInstanceHandler) checkAttributes(false, false, false, false, true, true); } /** * tests whether the scheme declares a serialVersionUID. */ public void testSerialVersionUID() { boolean[] result; result = m_Tester.declaresSerialVersionUID(); if (!result[0]) fail("Doesn't declare serialVersionUID!"); } /** * tests whether the scheme handles instance weights correctly * * @see CheckAttributeSelection#instanceWeights(boolean, boolean, boolean, boolean, boolean, boolean, int) * @see CheckAttributeSelection#testsPerClassType(int, boolean, boolean) */ public void testInstanceWeights() { boolean[] result; int i; if (m_weightedInstancesHandler) { for (i = FIRST_CLASSTYPE; i <= LAST_CLASSTYPE; i++) { // does the scheme support this type of class at all? if (!canPredict(i)) continue; result = m_Tester.instanceWeights( m_NominalPredictors[i], m_NumericPredictors[i], m_StringPredictors[i], m_DatePredictors[i], m_RelationalPredictors[i], m_multiInstanceHandler, i); if (!result[0]) System.err.println("Error handling instance weights (" + getClassTypeString(i) + " class)!"); } } } /** * tests whether scheme handles N classes * * @see CheckAttributeSelection#canHandleNClasses(boolean, boolean, boolean, boolean, boolean, boolean, int) * @see CheckAttributeSelection#testsPerClassType(int, boolean, boolean) * @see #m_NClasses */ public void testNClasses() { boolean[] result; if (!canPredict(Attribute.NOMINAL)) return; result = m_Tester.canHandleNClasses( m_NominalPredictors[Attribute.NOMINAL], m_NumericPredictors[Attribute.NOMINAL], m_StringPredictors[Attribute.NOMINAL], m_DatePredictors[Attribute.NOMINAL], m_RelationalPredictors[Attribute.NOMINAL], m_multiInstanceHandler, m_NClasses); if (!result[0] && !result[1]) fail("Error handling " + m_NClasses + " classes!"); } /** * checks whether the scheme can handle the class attribute at a given * position (0-based index, -1 means last). * * @param type the class type * @param position the position of the class attribute (0-based, -1 means last) * @return true if the scheme can handle it */ protected boolean checkClassAsNthAttribute(int type, int position) { boolean[] result; String indexStr; result = m_Tester.canHandleClassAsNthAttribute( m_NominalPredictors[type], m_NumericPredictors[type], m_StringPredictors[type], m_DatePredictors[type], m_RelationalPredictors[type], m_multiInstanceHandler, type, position); if (position == -1) indexStr = "last"; else indexStr = (position + 1) + "."; if (!result[0] && !result[1]) fail("Error handling class as " + indexStr + " attribute (" + getClassTypeString(type) + " class)!"); return result[0]; } /** * Tests whether the scheme can handle class attributes as Nth * attribute. In case of multi-instance handler it performs no tests, * since the multi-instance data has a fixed format (bagID,bag,class). * * @see CheckAttributeSelection#canHandleClassAsNthAttribute(boolean, boolean, boolean, boolean, boolean, boolean, int, int) * @see CheckAttributeSelection#testsPerClassType(int, boolean, boolean) */ public void testClassAsNthAttribute() { int i; // multi-Instance data has fixed format! if (m_multiInstanceHandler) return; for (i = FIRST_CLASSTYPE; i <= LAST_CLASSTYPE; i++) { // does the scheme support this type of class at all? if (!canPredict(i)) continue; // first attribute m_handleClassAsFirstAttribute[i] = checkClassAsNthAttribute(i, 0); // second attribute m_handleClassAsSecondAttribute[i] = checkClassAsNthAttribute(i, 1); } } /** * tests whether the scheme can handle zero training instances * * @see CheckAttributeSelection#canHandleZeroTraining(boolean, boolean, boolean, boolean, boolean, boolean, int) * @see CheckAttributeSelection#testsPerClassType(int, boolean, boolean) */ public void testZeroTraining() { boolean[] result; int i; for (i = FIRST_CLASSTYPE; i <= LAST_CLASSTYPE; i++) { // does the scheme support this type of class at all? if (!canPredict(i)) continue; result = m_Tester.canHandleZeroTraining( m_NominalPredictors[i], m_NumericPredictors[i], m_StringPredictors[i], m_DatePredictors[i], m_RelationalPredictors[i], m_multiInstanceHandler, i); if (!result[0] && !result[1]) fail("Error handling zero training instances (" + getClassTypeString(i) + " class)!"); } } /** * checks whether the scheme can handle the given percentage of * missing predictors * * @param type the class type * @param percent the percentage of missing predictors * @param allowFail if true a fail statement may be executed * @return true if the scheme can handle it */ protected boolean checkMissingPredictors(int type, int percent, boolean allowFail) { boolean[] result; result = m_Tester.canHandleMissing( m_NominalPredictors[type], m_NumericPredictors[type], m_StringPredictors[type], m_DatePredictors[type], m_RelationalPredictors[type], m_multiInstanceHandler, type, true, false, percent); if (allowFail) { if (!result[0] && !result[1]) fail("Error handling " + percent + "% missing predictors (" + getClassTypeString(type) + " class)!"); } return result[0]; } /** * tests whether the scheme can handle missing predictors (20% and 100%) * * @see CheckAttributeSelection#canHandleMissing(boolean, boolean, boolean, boolean, boolean, boolean, int, boolean, boolean, int) * @see CheckAttributeSelection#testsPerClassType(int, boolean, boolean) */ public void testMissingPredictors() { int i; for (i = FIRST_CLASSTYPE; i <= LAST_CLASSTYPE; i++) { // does the scheme support this type of class at all? if (!canPredict(i)) continue; // 20% missing checkMissingPredictors(i, 20, true); // 100% missing if (m_handleMissingPredictors[i]) checkMissingPredictors(i, 100, true); } } /** * checks whether the scheme can handle the given percentage of * missing class labels * * @param type the class type * @param percent the percentage of missing class labels * @param allowFail if true a fail statement may be executed * @return true if the scheme can handle it */ protected boolean checkMissingClass(int type, int percent, boolean allowFail) { boolean[] result; result = m_Tester.canHandleMissing( m_NominalPredictors[type], m_NumericPredictors[type], m_StringPredictors[type], m_DatePredictors[type], m_RelationalPredictors[type], m_multiInstanceHandler, type, false, true, percent); if (allowFail) { if (!result[0] && !result[1]) fail("Error handling " + percent + "% missing class labels (" + getClassTypeString(type) + " class)!"); } return result[0]; } /** * tests whether the scheme can handle missing class values (20% and * 100%) * * @see CheckAttributeSelection#canHandleMissing(boolean, boolean, boolean, boolean, boolean, boolean, int, boolean, boolean, int) * @see CheckAttributeSelection#testsPerClassType(int, boolean, boolean) */ public void testMissingClass() { int i; for (i = FIRST_CLASSTYPE; i <= LAST_CLASSTYPE; i++) { // does the scheme support this type of class at all? if (!canPredict(i)) continue; // 20% missing checkMissingClass(i, 20, true); // 100% missing if (m_handleMissingClass[i]) checkMissingClass(i, 100, true); } } /** * tests whether the scheme correctly initializes in the * search method * * @see CheckAttributeSelection#correctSearchInitialisation(boolean, boolean, boolean, boolean, boolean, boolean, int) * @see CheckAttributeSelection#testsPerClassType(int, boolean, boolean) */ public void testBuildInitialization() { boolean[] result; int i; for (i = FIRST_CLASSTYPE; i <= LAST_CLASSTYPE; i++) { // does the scheme support this type of class at all? if (!canPredict(i)) continue; result = m_Tester.correctSearchInitialisation( m_NominalPredictors[i], m_NumericPredictors[i], m_StringPredictors[i], m_DatePredictors[i], m_RelationalPredictors[i], m_multiInstanceHandler, i); if (!result[0] && !result[1]) fail("Incorrect build initialization (" + getClassTypeString(i) + " class)!"); } } /** * tests whether the scheme alters the training set during training. * * @see CheckAttributeSelection#datasetIntegrity(boolean, boolean, boolean, boolean, boolean, boolean, int, boolean, boolean) * @see CheckAttributeSelection#testsPerClassType(int, boolean, boolean) */ public void testDatasetIntegrity() { boolean[] result; int i; for (i = FIRST_CLASSTYPE; i <= LAST_CLASSTYPE; i++) { // does the scheme support this type of class at all? if (!canPredict(i)) continue; result = m_Tester.datasetIntegrity( m_NominalPredictors[i], m_NumericPredictors[i], m_StringPredictors[i], m_DatePredictors[i], m_RelationalPredictors[i], m_multiInstanceHandler, i, m_handleMissingPredictors[i], m_handleMissingClass[i]); if (!result[0] && !result[1]) fail("Dataset is altered during training (" + getClassTypeString(i) + " class)!"); } } /** * Builds a model using the current scheme using the given data. * * @param data the instances to test the selection scheme on * @return a string containing the results. */ protected String useScheme(Instances data) throws Exception { AttributeSelection attsel = null; try { attsel = new AttributeSelection(); attsel.setSearch(m_Search); attsel.setEvaluator(m_Evaluator); attsel.setSeed(42); } catch (Exception e) { e.printStackTrace(); fail("Problem setting up attribute selection: " + e); } attsel.SelectAttributes(data); return attsel.toResultsString(); } /** * Provides a hook for derived classes to further modify the data. Currently, * the data is just passed through. * * @param data the data to process * @return the processed data */ protected Instances process(Instances data) { return data; } /** * Runs a regression test -- this checks that the output of the tested * object matches that in a reference version. When this test is * run without any pre-existing reference output, the reference version * is created. */ public void testRegression() throws Exception { int i; boolean succeeded; Regression reg; Instances train; // don't bother if not working correctly if (m_Tester.hasClasspathProblems()) return; reg = new Regression(this.getClass()); succeeded = false; train = null; for (i = FIRST_CLASSTYPE; i <= LAST_CLASSTYPE; i++) { // does the scheme support this type of class at all? if (!canPredict(i)) continue; train = m_Tester.makeTestDataset( 42, m_Tester.getNumInstances(), m_NominalPredictors[i] ? 2 : 0, m_NumericPredictors[i] ? 1 : 0, m_StringPredictors[i] ? 1 : 0, m_DatePredictors[i] ? 1 : 0, m_RelationalPredictors[i] ? 1 : 0, 2, i, m_multiInstanceHandler); try { m_RegressionResults[i] = useScheme(train); succeeded = true; reg.println(m_RegressionResults[i]); } catch (Exception e) { String msg = e.getMessage().toLowerCase(); if (msg.indexOf("not in classpath") > -1) return; m_RegressionResults[i] = null; } } if (!succeeded) { fail("Problem during regression testing: no successful predictions for any class type"); } try { String diff = reg.diff(); if (diff == null) { System.err.println("Warning: No reference available, creating."); } else if (!diff.equals("")) { fail("Regression test failed. Difference:\n" + diff); } } catch (java.io.IOException ex) { fail("Problem during regression testing.\n" + ex); } } /** * tests the listing of the options */ public void testListOptions() { if (m_OptionTester.getOptionHandler() != null) { if (!m_OptionTester.checkListOptions()) fail("Options cannot be listed via listOptions."); } } /** * tests the setting of the options */ public void testSetOptions() { if (m_OptionTester.getOptionHandler() != null) { if (!m_OptionTester.checkSetOptions()) fail("setOptions method failed."); } } /** * tests whether the default settings are processed correctly */ public void testDefaultOptions() { if (m_OptionTester.getOptionHandler() != null) { if (!m_OptionTester.checkDefaultOptions()) fail("Default options were not processed correctly."); } } /** * tests whether there are any remaining options */ public void testRemainingOptions() { if (m_OptionTester.getOptionHandler() != null) { if (!m_OptionTester.checkRemainingOptions()) fail("There were 'left-over' options."); } } /** * tests the whether the user-supplied options stay the same after setting. * getting, and re-setting again. * * @see #getOptionTester() */ public void testCanonicalUserOptions() { if (m_OptionTester.getOptionHandler() != null) { if (!m_OptionTester.checkCanonicalUserOptions()) fail("setOptions method failed"); } } /** * tests the resetting of the options to the default ones */ public void testResettingOptions() { if (m_OptionTester.getOptionHandler() != null) { if (!m_OptionTester.checkSetOptions()) fail("Resetting of options failed"); } } /** * tests for a globalInfo method */ public void testGlobalInfo() { if (!m_GOETester.checkGlobalInfo()) fail("No globalInfo method"); } /** * tests the tool tips */ public void testToolTips() { if (!m_GOETester.checkToolTips()) fail("Tool tips inconsistent"); } }