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Posted to dev@commons.apache.org by to...@apache.org on 2003/05/29 21:41:32 UTC
cvs commit: jakarta-commons-sandbox/math/src/test/org/apache/commons/math/beans Patient.java VitalStats.java
tobrien 2003/05/29 12:41:32
Modified: math project.xml
math/src/java/org/apache/commons/math
ListUnivariateImpl.java
Added: math/src/java/org/apache/commons/math
BeanListUnivariateImpl.java
math/src/test/org/apache/commons/math
BeanListUnivariateImplTest.java
math/src/test/org/apache/commons/math/beans Patient.java
VitalStats.java
Log:
Addition of a BeanListUnivariateImpl which can gather univariate statistics on a
List of JavaBeans. This implementation extends the ListUnivariateImpl, and uses the
PropertyUtils classes from commons-beanutils. With this implementation, the following
is possible:
List persons = new ArrayList();
// populate array with 100 persons
Univariate ageU = new BeanListUnivariateImpl( persons, "age" );
Univariate incomeU = new BeanListUnivariateImpl( persons, "jobInfo.income" );
System.out.println( "Mean age is: " + ageU.getMean() );
System.out.println( "Mean income is: " + incomeU.getMean() );
Better error handling is needed near our use of PropertyUtils.
This patch introduces a dependency on commons-beanutils, which in turn depends
on commons-collections and commons-logging.
Revision Changes Path
1.11 +17 -0 jakarta-commons-sandbox/math/project.xml
Index: project.xml
===================================================================
RCS file: /home/cvs/jakarta-commons-sandbox/math/project.xml,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- project.xml 26 May 2003 17:29:35 -0000 1.10
+++ project.xml 29 May 2003 19:41:31 -0000 1.11
@@ -34,6 +34,23 @@
</developer>
</developers>
+ <dependencies>
+
+ <dependency>
+ <id>commons-beanutils</id>
+ <version>1.5</version>
+ </dependency>
+ <dependency>
+ <id>commons-collections</id>
+ <version>2.1</version>
+ </dependency>
+ <dependency>
+ <id>commons-logging</id>
+ <version>1.0.3</version>
+ </dependency>
+
+ </dependencies>
+
<contributors>
<contributor>
<name>Phil Steitz</name>
1.6 +24 -12 jakarta-commons-sandbox/math/src/java/org/apache/commons/math/ListUnivariateImpl.java
Index: ListUnivariateImpl.java
===================================================================
RCS file: /home/cvs/jakarta-commons-sandbox/math/src/java/org/apache/commons/math/ListUnivariateImpl.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- ListUnivariateImpl.java 26 May 2003 17:40:20 -0000 1.5
+++ ListUnivariateImpl.java 29 May 2003 19:41:31 -0000 1.6
@@ -78,8 +78,9 @@
*/
public double[] getValues() {
- // If we've got a windowSize, we might not care about the entire list.
- List effectiveList = list;
+ int startIndex = 0;
+ int endIndex = list.size() - 1;
+
// If the window size is not INFINITE_WINDOW AND
// the current list is larger that the window size, we need to
@@ -87,17 +88,14 @@
// as definied by windowSize
if (windowSize != Univariate.INFINITE_WINDOW &&
windowSize < list.size()) {
- effectiveList = list.subList((list.size() - 1) - windowSize,
- (list.size()-1));
+ startIndex = (list.size() - 1) - windowSize;
}
// Create an array to hold all values
- double[] copiedArray = new double[effectiveList.size()];
+ double[] copiedArray = new double[list.size() - startIndex];
- int i = 0;
- Iterator it = effectiveList.iterator();
- while(it.hasNext()) {
- Number n = (Number) it.next();
+ for( int i = startIndex; i <= endIndex; i++ ) {
+ Number n = (Number) getInternalIndex( i );
copiedArray[i] = n.doubleValue();
i++;
}
@@ -116,13 +114,12 @@
int calcIndex = (list.size() - windowSize) + index;
- Number n = (Number) list.get(calcIndex);
+ Number n = (Number) getInternalIndex(calcIndex);
value = n.doubleValue();
} else {
- Number n = (Number) list.get(index);
+ Number n = (Number) getInternalIndex(index);
value = n.doubleValue();
}
- System.out.println( "Returning value: " + value );
return value;
}
@@ -170,5 +167,20 @@
*/
public void setWindowSize(int windowSize) {
this.windowSize = windowSize;
+ }
+
+ /**
+ * This function exists to support the function of classes which
+ * extend the ListUnivariateImpl.
+ *
+ * @param index The location of the value in the internal List
+ * @return A Number object representing the value at a given
+ * index
+ */
+ protected Number getInternalIndex(int index) {
+
+ Number n = (Number) list.get( index );
+ return n;
+
}
}
1.1 jakarta-commons-sandbox/math/src/java/org/apache/commons/math/BeanListUnivariateImpl.java
Index: BeanListUnivariateImpl.java
===================================================================
/* ====================================================================
* The Apache Software License, Version 1.1
*
* Copyright (c) 2003 The Apache Software Foundation. All rights
* reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
*
* 1. Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in
* the documentation and/or other materials provided with the
* distribution.
*
* 3. The end-user documentation included with the redistribution, if
* any, must include the following acknowlegement:
* "This product includes software developed by the
* Apache Software Foundation (http://www.apache.org/)."
* Alternately, this acknowlegement may appear in the software itself,
* if and wherever such third-party acknowlegements normally appear.
*
* 4. The names "The Jakarta Project", "Commons", and "Apache Software
* Foundation" must not be used to endorse or promote products derived
* from this software without prior written permission. For written
* permission, please contact apache@apache.org.
*
* 5. Products derived from this software may not be called "Apache"
* nor may "Apache" appear in their names without prior written
* permission of the Apache Software Foundation.
*
* THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
* WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
* OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
* ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
* USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
* OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
* SUCH DAMAGE.
* ====================================================================
*
* This software consists of voluntary contributions made by many
* individuals on behalf of the Apache Software Foundation. For more
* information on the Apache Software Foundation, please see
* <http://www.apache.org/>.
*/
package org.apache.commons.math;
import java.util.Iterator;
import java.util.List;
import org.apache.commons.beanutils.PropertyUtils;
/**
* This implementation of StoreUnivariate uses commons-beanutils to gather
* univariate statistics for a List of Java Beans by property. This
* implementation uses beanutils' PropertyUtils to get a simple, nested,
* indexed, mapped, or combined property from an element of a List.
*
* @author <a href="mailto:tobrien@apache.org">Tim O'Brien</a>
*/
public class BeanListUnivariateImpl extends ListUnivariateImpl {
private String propertyName;
public BeanListUnivariateImpl(List list) {
super( list );
}
public BeanListUnivariateImpl(List list, String propertyName) {
super( list );
setPropertyName( propertyName );
}
public String getPropertyName() {
return propertyName;
}
public void setPropertyName(String propertyName) {
System.out.println( "Set prop name; " + propertyName );
this.propertyName = propertyName;
}
/* (non-Javadoc)
* @see org.apache.commons.math.Univariate#addValue(double)
*/
public void addValue(double v) {
String msg = "The BeanListUnivariateImpl does not accept values " +
"through the addValue method. Because elements of this list " +
"are JavaBeans, one must be sure to set the 'propertyName' " +
"property and add new Beans to the underlying list via the " +
"addBean(Object bean) method";
throw new UnsupportedOperationException( msg );
}
/**
* Adds a bean to this list.
*
* @param bean Bean to add to the list
*/
public void addObject(Object bean) {
list.add(bean);
}
/**
* Reads the property of an element in the list.
*
* @param index The location of the value in the internal List
* @return A Number object representing the value at a given
* index
*/
protected Number getInternalIndex(int index) {
try {
Number n = (Number) PropertyUtils.getProperty( list.get( index ),
propertyName );
return n;
} catch( Exception e ) {
// TODO: We could use a better strategy for error handling
// here.
// This is a somewhat foolish design decision, but until
// we figure out what needs to be done, let's return NaN
return new Double(Double.NaN);
}
}
}
1.1 jakarta-commons-sandbox/math/src/test/org/apache/commons/math/BeanListUnivariateImplTest.java
Index: BeanListUnivariateImplTest.java
===================================================================
/* ====================================================================
* The Apache Software License, Version 1.1
*
* Copyright (c) 2003 The Apache Software Foundation. All rights
* reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
*
* 1. Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in
* the documentation and/or other materials provided with the
* distribution.
*
* 3. The end-user documentation included with the redistribution, if
* any, must include the following acknowlegement:
* "This product includes software developed by the
* Apache Software Foundation (http://www.apache.org/)."
* Alternately, this acknowlegement may appear in the software itself,
* if and wherever such third-party acknowlegements normally appear.
*
* 4. The names "The Jakarta Project", "Commons", and "Apache Software
* Foundation" must not be used to endorse or promote products derived
* from this software without prior written permission. For written
* permission, please contact apache@apache.org.
*
* 5. Products derived from this software may not be called "Apache"
* nor may "Apache" appear in their names without prior written
* permission of the Apache Software Foundation.
*
* THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
* WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
* OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
* ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
* USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
* OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
* SUCH DAMAGE.
* ====================================================================
*
* This software consists of voluntary contributions made by many
* individuals on behalf of the Apache Software Foundation. For more
* information on the Apache Software Foundation, please see
* <http://www.apache.org/>.
*/
package org.apache.commons.math;
import java.util.ArrayList;
import java.util.List;
import junit.framework.Test;
import junit.framework.TestCase;
import junit.framework.TestSuite;
import org.apache.commons.math.beans.*;
/**
* Test cases for the {@link BeanListUnivariateImpl} class.
*
* @author <a href="mailto:tobrien@apache.org">Tim O'Brien</a>
* @version $Revision: 1.1 $ $Date: 2003/05/29 19:41:31 $
*/
public final class BeanListUnivariateImplTest extends TestCase {
private List patientList = null;
private double tolerance = Double.MIN_VALUE;
public BeanListUnivariateImplTest(String name) {
super(name);
}
public void setUp() {
patientList = new ArrayList();
// Create and add patient bean 1
VitalStats vs1 = new VitalStats( new Double(120.0),
new Double(96.4) );
Patient p1 = new Patient( vs1, new Integer( 35 ) );
patientList.add( p1 );
// Create and add patient bean 2
VitalStats vs2 = new VitalStats( new Double(70.0),
new Double(97.4) );
Patient p2 = new Patient( vs2, new Integer( 23 ) );
patientList.add( p2 );
// Create and add patient bean 3
VitalStats vs3 = new VitalStats( new Double(90.0),
new Double(98.6) );
Patient p3 = new Patient( vs3, new Integer( 42 ) );
patientList.add( p3 );
}
public static Test suite() {
TestSuite suite = new TestSuite(BeanListUnivariateImplTest.class);
suite.setName("Freq Tests");
return suite;
}
/** test stats */
public void testStats() {
StoreUnivariate u = new BeanListUnivariateImpl( patientList );
assertEquals("total count",3,u.getN(),tolerance);
u.clear();
assertEquals("total count",0,u.getN(),tolerance);
}
public void testPropStats() {
StoreUnivariate heartU = new BeanListUnivariateImpl( patientList,
"vitalStats.heartRate" );
assertEquals( "Mean heart rate unexpected", 93.333,
heartU.getMean(), 0.001 );
assertEquals( "Max heart rate unexpected", 120.0,
heartU.getMax(), 0.001 );
StoreUnivariate ageU = new BeanListUnivariateImpl( patientList,
"age" );
assertEquals( "Mean age unexpected", 33.333,
ageU.getMean(), 0.001 );
assertEquals( "Max age unexpected", 42.0,
ageU.getMax(), 0.001 );
}
/* public void testN0andN1Conditions() throws Exception {
List list = new ArrayList();
StoreUnivariate u = new ListUnivariateImpl( list );
assertTrue("Mean of n = 0 set should be NaN", Double.isNaN( u.getMean() ) );
assertTrue("Standard Deviation of n = 0 set should be NaN", Double.isNaN( u.getStandardDeviation() ) );
assertTrue("Variance of n = 0 set should be NaN", Double.isNaN(u.getVariance() ) );
list.add( new Double(one));
assertTrue( "Mean of n = 1 set should be value of single item n1", u.getMean() == one);
assertTrue( "StdDev of n = 1 set should be zero, instead it is: " + u.getStandardDeviation(), u.getStandardDeviation() == 0);
assertTrue( "Variance of n = 1 set should be zero", u.getVariance() == 0);
}
public void testSkewAndKurtosis() {
StoreUnivariate u = new StoreUnivariateImpl();
double[] testArray = { 12.5, 12, 11.8, 14.2, 14.9, 14.5, 21, 8.2, 10.3, 11.3, 14.1,
9.9, 12.2, 12, 12.1, 11, 19.8, 11, 10, 8.8, 9, 12.3 };
for( int i = 0; i < testArray.length; i++) {
u.addValue( testArray[i]);
}
assertEquals("mean", 12.40455, u.getMean(), 0.0001);
assertEquals("variance", 10.00236, u.getVariance(), 0.0001);
assertEquals("skewness", 1.437424, u.getSkewness(), 0.0001);
assertEquals("kurtosis", 2.37719, u.getKurtosis(), 0.0001);
}
public void testProductAndGeometricMean() throws Exception {
ListUnivariateImpl u = new ListUnivariateImpl(new ArrayList());
u.setWindowSize(10);
u.addValue( 1.0 );
u.addValue( 2.0 );
u.addValue( 3.0 );
u.addValue( 4.0 );
assertEquals( "Product not expected", 24.0, u.getProduct(), Double.MIN_VALUE );
assertEquals( "Geometric mean not expected", 2.213364, u.getGeometricMean(), 0.00001 );
// Now test rolling - UnivariateImpl should discount the contribution
// of a discarded element
for( int i = 0; i < 10; i++ ) {
u.addValue( i + 2 );
}
// Values should be (2,3,4,5,6,7,8,9,10,11)
assertEquals( "Product not expected", 39916800.0, u.getProduct(), 0.00001 );
assertEquals( "Geometric mean not expected", 5.755931, u.getGeometricMean(), 0.00001 );
} */
}
1.1 jakarta-commons-sandbox/math/src/test/org/apache/commons/math/beans/Patient.java
Index: Patient.java
===================================================================
/* ====================================================================
* The Apache Software License, Version 1.1
*
* Copyright (c) 2003 The Apache Software Foundation. All rights
* reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
*
* 1. Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in
* the documentation and/or other materials provided with the
* distribution.
*
* 3. The end-user documentation included with the redistribution, if
* any, must include the following acknowlegement:
* "This product includes software developed by the
* Apache Software Foundation (http://www.apache.org/)."
* Alternately, this acknowlegement may appear in the software itself,
* if and wherever such third-party acknowlegements normally appear.
*
* 4. The names "The Jakarta Project", "Commons", and "Apache Software
* Foundation" must not be used to endorse or promote products derived
* from this software without prior written permission. For written
* permission, please contact apache@apache.org.
*
* 5. Products derived from this software may not be called "Apache"
* nor may "Apache" appear in their names without prior written
* permission of the Apache Software Foundation.
*
* THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
* WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
* OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
* ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
* USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
* OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
* SUCH DAMAGE.
* ====================================================================
*
* This software consists of voluntary contributions made by many
* individuals on behalf of the Apache Software Foundation. For more
* information on the Apache Software Foundation, please see
* <http://www.apache.org/>.
*/
package org.apache.commons.math.beans;
public class Patient {
private VitalStats vitalStats;
private Integer age;
public Patient() {
}
public Patient(VitalStats vitalStats, Integer age) {
setVitalStats( vitalStats );
setAge( age );
}
public VitalStats getVitalStats() {
return( vitalStats );
}
public void setVitalStats(VitalStats vitalStats) {
this.vitalStats = vitalStats;
}
public Integer getAge() {
return age;
}
public void setAge(Integer age) {
this.age = age;
}
}
1.1 jakarta-commons-sandbox/math/src/test/org/apache/commons/math/beans/VitalStats.java
Index: VitalStats.java
===================================================================
/* ====================================================================
* The Apache Software License, Version 1.1
*
* Copyright (c) 2003 The Apache Software Foundation. All rights
* reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
*
* 1. Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in
* the documentation and/or other materials provided with the
* distribution.
*
* 3. The end-user documentation included with the redistribution, if
* any, must include the following acknowlegement:
* "This product includes software developed by the
* Apache Software Foundation (http://www.apache.org/)."
* Alternately, this acknowlegement may appear in the software itself,
* if and wherever such third-party acknowlegements normally appear.
*
* 4. The names "The Jakarta Project", "Commons", and "Apache Software
* Foundation" must not be used to endorse or promote products derived
* from this software without prior written permission. For written
* permission, please contact apache@apache.org.
*
* 5. Products derived from this software may not be called "Apache"
* nor may "Apache" appear in their names without prior written
* permission of the Apache Software Foundation.
*
* THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
* WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
* OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
* ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
* USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
* OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
* SUCH DAMAGE.
* ====================================================================
*
* This software consists of voluntary contributions made by many
* individuals on behalf of the Apache Software Foundation. For more
* information on the Apache Software Foundation, please see
* <http://www.apache.org/>.
*/
package org.apache.commons.math.beans;
public class VitalStats {
private Double heartrate;
private Double temperature;
public VitalStats() {
}
public VitalStats(Double heartrate, Double temperature) {
setHeartRate( heartrate );
setTemperature( temperature );
}
public Double getHeartRate() {
return heartrate;
}
public void setHeartRate(Double heartrate) {
this.heartrate = heartrate;
}
public Double getTemperature() {
return temperature;
}
public void setTemperature(Double temperature) {
this.temperature = temperature;
}
}
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