/*
* ParameterParser.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.inference.model;
import java.io.File;
import java.io.IOException;
import java.util.List;
import dr.inference.trace.LogFileTraces;
import dr.inference.trace.TraceException;
import dr.math.MathUtils;
import dr.math.distributions.Distribution;
import dr.xml.*;
/**
* Parses a multi-dimensional continuous parameter.
*
* @author Alexei Drummond
* @author Andrew Rambaut
*
* @version $Id: ParameterParser.java,v 1.12 2005/05/24 20:26:00 rambaut Exp $
*/
public class ParameterParser extends dr.xml.AbstractXMLObjectParser {
public static final String UPPER = "upper";
public static final String LOWER = "lower";
public static final String DIMENSION = "dimension";
public static final String VALUE = "value";
public static final String PARAMETER = "parameter";
public static final String RANDOMIZE = "randomize";
public static final String FILENAME = "fileName";
public static final String BURNIN = "burnin";
public static final String PARAMETERCOLUMN = "parameterColumn";
public String getParserName() {
return PARAMETER;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
double[] values = null;
double[] uppers;
double[] lowers;
if( xo.hasAttribute(DIMENSION) ) {
values = new double[xo.getIntegerAttribute(DIMENSION)];
}
if ( xo.hasAttribute(FILENAME)) {
//read samples from a file (used for a reference prior) and calculate the mean
String fileName = xo.getStringAttribute(FILENAME);
File file = new File(fileName);
fileName = file.getName();
String parent = file.getParent();
if (!file.isAbsolute()) {
parent = System.getProperty("user.dir");
}
file = new File(parent, fileName);
fileName = file.getAbsolutePath();
String columnName = "";
if ( xo.hasAttribute(PARAMETERCOLUMN)) {
columnName = xo.getStringAttribute(PARAMETERCOLUMN);
} else {
throw new XMLParseException("when providing a file name you must provide a parameter column as well");
}
//if a number for the burnin is not given, use 0 ...
int burnin;
if ( xo.hasAttribute(BURNIN)) {
burnin = xo.getIntegerAttribute(BURNIN);
} else {
burnin = 0;
}
LogFileTraces traces = new LogFileTraces(fileName, file);
List parameterSamples = null;
try {
traces.loadTraces();
traces.setBurnIn(burnin);
int traceIndexParameter = -1;
for (int i = 0; i < traces.getTraceCount(); i++) {
String traceName = traces.getTraceName(i);
if (traceName.trim().equals(columnName)) {
traceIndexParameter = i;
}
}
if (traceIndexParameter == -1) {
throw new XMLParseException("Column '" + columnName + "' can not be found for " + getParserName() + " element.");
}
parameterSamples = traces.getValues(traceIndexParameter);
} catch (TraceException e) {
throw new XMLParseException(e.getMessage());
} catch (IOException ioe) {
throw new XMLParseException(ioe.getMessage());
}
values = new double[1];
for (int i = 0, stop = parameterSamples.size(); i < stop; i++) {
values[0] += ((Double)parameterSamples.get(i))/((double)stop);
}
System.out.println("Number of samples: " + parameterSamples.size());
System.out.println("Parameter mean: " + values[0]);
} else if( xo.hasAttribute(VALUE) ) {
if( values == null ) {
values = xo.getDoubleArrayAttribute(VALUE);
} else {
double[] v = xo.getDoubleArrayAttribute(VALUE);
if( v.length == values.length ) {
System.arraycopy(v, 0, values, 0, v.length);
} else if( v.length == 1 ) {
for(int i = 0; i < values.length; i++) {
values[i] = v[0];
}
} else {
throw new XMLParseException("value string must have 1 value or dimension values");
}
}
} else {
if( xo.hasAttribute(DIMENSION) ) {
values = new double[xo.getIntegerAttribute(DIMENSION)];
} else {
// parameter dimension will get set correctly by TreeModel presumably.
if (!xo.hasChildNamed(RANDOMIZE)) {
return new Parameter.Default(1);
}
values = new double[1];
values[0] = 1.0;
}
}
uppers = new double[values.length];
for(int i = 0; i < values.length; i++) {
uppers[i] = Double.POSITIVE_INFINITY;
}
lowers = new double[values.length];
for(int i = 0; i < values.length; i++) {
lowers[i] = Double.NEGATIVE_INFINITY;
}
if( xo.hasAttribute(UPPER) ) {
double[] v = xo.getDoubleArrayAttribute(UPPER);
if( v.length == uppers.length ) {
System.arraycopy(v, 0, uppers, 0, v.length);
} else if( v.length == 1 ) {
for(int i = 0; i < uppers.length; i++) {
uppers[i] = v[0];
}
} else {
throw new XMLParseException("uppers string must have 1 value or dimension values");
}
}
if( xo.hasAttribute(LOWER) ) {
double[] v = xo.getDoubleArrayAttribute(LOWER);
if( v.length == lowers.length ) {
System.arraycopy(v, 0, lowers, 0, v.length);
} else if( v.length == 1 ) {
for(int i = 0; i < lowers.length; i++) {
lowers[i] = v[0];
}
} else {
throw new XMLParseException("lowers string must have 1 value or dimension values");
}
}
// assert uppers != null && lowers != null;
if( (uppers.length != values.length) ) {
throw new XMLParseException("value and upper limit strings have different dimension, in parameter");
}
if( (lowers.length != values.length) ) {
throw new XMLParseException("value and lower limit strings have different dimension, in parameter");
}
// check if uppers and lowers are consistent
for(int i = 0; i < values.length; i++) {
if( uppers[i] < lowers[i] ) {
throw new XMLParseException("upper is lower than lower, in parameter");
}
}
if (xo.hasChildNamed(RANDOMIZE)) {
Distribution distribution = (Distribution) xo.getChild(RANDOMIZE).getChild(Distribution.class);
for (int i = 0; i < values.length; i++) {
do {
// Not an efficient way to draw random variables, but this is currently the only general interface
values[i] = distribution.quantile(MathUtils.nextDouble());
} while (values[i] < lowers[i] || values[i] > uppers[i]);
}
} else {
// make values consistent with bounds
for(int i = 0; i < values.length; i++) {
if( uppers[i] < values[i] ) values[i] = uppers[i];
}
for(int i = 0; i < values.length; i++) {
if (lowers[i] > values[i]) values[i] = lowers[i];
}
}
Parameter param = new Parameter.Default(values.length);
for(int i = 0; i < values.length; i++) {
param.setParameterValue(i, values[i]);
}
param.addBounds(new Parameter.DefaultBounds(uppers, lowers));
return param;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
AttributeRule.newDoubleArrayRule(VALUE, true),
AttributeRule.newIntegerRule(DIMENSION, true),
AttributeRule.newStringRule(FILENAME, true),
AttributeRule.newStringRule(PARAMETERCOLUMN, true),
AttributeRule.newIntegerRule(BURNIN, true),
AttributeRule.newDoubleArrayRule(UPPER, true),
AttributeRule.newDoubleArrayRule(LOWER, true),
new ElementRule(RANDOMIZE, new XMLSyntaxRule[] {
new ElementRule(Distribution.class),
},true),
};
public String getParserDescription() {
return "A real-valued parameter of one or more dimensions.";
}
public Class getReturnType() {
return Parameter.class;
}
static public void replaceParameter(XMLObject xo, Parameter newParam) throws XMLParseException {
for (int i = 0; i < xo.getChildCount(); i++) {
if (xo.getChild(i) instanceof Parameter) {
XMLObject rxo;
Object obj = xo.getRawChild(i);
if (obj instanceof Reference ) {
rxo = ((Reference) obj).getReferenceObject();
} else if (obj instanceof XMLObject) {
rxo = (XMLObject) obj;
} else {
throw new XMLParseException("object reference not available");
}
if (rxo.getChildCount() > 0) {
throw new XMLParseException("No child elements allowed in parameter element.");
}
if (rxo.hasAttribute(XMLParser.IDREF)) {
throw new XMLParseException("References to " + xo.getName() + " parameters are not allowed in treeModel.");
}
if (rxo.hasAttribute(VALUE)) {
throw new XMLParseException("Parameters in " + xo.getName() + " have values set automatically.");
}
if (rxo.hasAttribute(UPPER)) {
throw new XMLParseException("Parameters in " + xo.getName() + " have bounds set automatically.");
}
if (rxo.hasAttribute(LOWER)) {
throw new XMLParseException("Parameters in " + xo.getName() + " have bounds set automatically.");
}
if (rxo.hasAttribute(XMLParser.ID)) {
newParam.setId(rxo.getStringAttribute(XMLParser.ID));
}
rxo.setNativeObject(newParam);
return;
}
}
}
// static public Parameter getParameter(XMLObject xo) throws XMLParseException {
//
// int paramCount = 0;
// Parameter param = null;
// for (int i = 0; i < xo.getChildCount(); i++) {
// if (xo.getChild(i) instanceof Parameter) {
// param = (Parameter) xo.getChild(i);
// paramCount += 1;
// }
// }
//
// if (paramCount == 0) {
// throw new XMLParseException("no parameter element in treeModel " + xo.getName() + " element");
// } else if (paramCount > 1) {
// throw new XMLParseException("More than one parameter element in treeModel " + xo.getName() + " element");
// }
//
// return param;
// }
}