timeBench.data.io.RConnector Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of timebench Show documentation
Show all versions of timebench Show documentation
TimeBench, a flexible, easy-to-use, and reusable software library written in Java that provides foundational data structures and algorithms for time- oriented data in Visual Analytics.
The newest version!
package timeBench.data.io;
import java.lang.reflect.InvocationTargetException;
import java.text.DateFormat;
import java.util.Arrays;
import java.util.Date;
import java.util.GregorianCalendar;
import java.util.TimeZone;
import org.apache.log4j.Logger;
import org.rosuda.REngine.REXP;
import org.rosuda.REngine.REXPDouble;
import org.rosuda.REngine.REXPMismatchException;
import org.rosuda.REngine.REngine;
import org.rosuda.REngine.REngineException;
import org.rosuda.REngine.REngineStdOutput;
import timeBench.calendar.Calendar;
import timeBench.calendar.CalendarFactory;
import timeBench.calendar.Granularity;
import timeBench.calendar.JavaDateCalendarManager;
import timeBench.data.TemporalDataException;
import timeBench.data.TemporalDataset;
import timeBench.data.TemporalElement;
import timeBench.data.TemporalElementStore;
import timeBench.data.TemporalObject;
/**
* XXX Should we (a) encapsulate REngine or (b) provide some static helper methods?
*
* TODO How handle R Exceptions?
*
* @author Rind
*/
public class RConnector {
public static final String RENGINE_IMPL = "org.rosuda.REngine.JRI.JRIEngine";
private static Logger logger = Logger.getLogger(RConnector.class);
private static RConnector instance;
private Calendar calendar = JavaDateCalendarManager.getSingleton().getDefaultCalendar();
// could be replaced by REngine.getLastEngine()
private REngine engine;
private RConnector() {
try {
if (logger.isInfoEnabled())
// show R console output in System.out
engine = REngine.engineForClass(RENGINE_IMPL, new String[] {
"--no-save", "--no-restore" }, new REngineStdOutput(),
false);
else
engine = REngine.engineForClass(RENGINE_IMPL);
} catch (ClassNotFoundException e) {
logger.error("unexpected exception", e);
} catch (NoSuchMethodException e) {
logger.error("unexpected exception", e);
} catch (IllegalAccessException e) {
logger.error("unexpected exception", e);
} catch (InvocationTargetException e) {
logger.error("unexpected exception", e);
}
}
public static synchronized RConnector getInstance(Calendar calendar) {
RConnector instance = getInstance();
instance.calendar = calendar;
return instance;
}
public static synchronized RConnector getInstance() {
if (null == instance)
instance = new RConnector();
return instance;
}
public double getDouble(String name) throws REXPMismatchException,
REngineException {
REXP x = engine.parseAndEval(name, null, true);
return x.asDouble();
}
public TemporalDataset getTemporalDataset(
String name) throws REngineException, REXPMismatchException,
TemporalDataException {
// check R class
REXP x = engine.parseAndEval("class(" + name + ")", null, true);
if (!x.isString())
throw new TemporalDataException("Unsupported R class: " + x);
logger.trace(x.asString());
// ts ... simplest R time series class
if ("ts".equals(x.asString())) {
int[] start = engine
.parseAndEval("start(" + name + ")", null, true)
.asIntegers();
double frequency = engine.parseAndEval("frequency(" + name + ")",
null, true).asDouble();
double[] data = engine.parseAndEval("as.vector(" + name + ")",
null, true).asDoubles();
logger.debug("ts with start: " + Arrays.toString(start)
+ ", frequency: " + frequency + ", obs: " + data.length);
// get calendar and granularity
Calendar calendar = JavaDateCalendarManager.getSingleton().getDefaultCalendar();
Granularity granularity = null;
if (Math.abs(frequency - 1.0) < 0.005
|| Math.abs(frequency - 0.1) < 0.005)
granularity = CalendarFactory.getSingleton().getGranularity(calendar,"Year","Top");
else if (Math.abs(frequency - 12.0) < 0.005)
granularity = CalendarFactory.getSingleton().getGranularity(calendar,"Month","Top");
else
throw new TemporalDataException(
"Unknown granularity. frequency: " + frequency);
// prepare a calendar
GregorianCalendar cal = new GregorianCalendar(
TimeZone.getTimeZone("UTC"));
cal.setTimeInMillis(0);
cal.set(GregorianCalendar.MONTH, 0);
cal.set(GregorianCalendar.DAY_OF_MONTH, 1);
cal.set(GregorianCalendar.HOUR_OF_DAY, 0);
cal.set(GregorianCalendar.MINUTE, 0);
cal.set(GregorianCalendar.YEAR, start[0]);
if (frequency - 12.0 < 0.05 && start.length > 1) {
// GregorianCalendar.MONTH starts with 0
cal.set(GregorianCalendar.MONTH, start[1] - 1);
}
// relational
TemporalDataset tmpds = new timeBench.data.TemporalDataset();
tmpds.addDataColumn(name, double.class, null);
// time indices are only used in log file to check our code
double[] time = new double[0];
DateFormat df = null;
if (logger.isTraceEnabled()) {
time = engine.parseAndEval(
"as.vector(time(" + name + "))", null, true).asDoubles();
df = DateFormat.getDateTimeInstance();
}
for (int i = 0; i < data.length; i++) {
long inf = cal.getTimeInMillis();
if (Math.abs(frequency - 12.0) < 0.005)
cal.add(GregorianCalendar.MONTH, 1);
else if (Math.abs(frequency - 0.1) < 0.005)
cal.add(GregorianCalendar.YEAR, 10);
else
cal.add(GregorianCalendar.YEAR, 1);
long sup = cal.getTimeInMillis() - 1;
if (logger.isTraceEnabled())
logger.trace("time from R: " + time[i] + " inf: "
+ df.format(new Date(inf)) + " sup: "
+ df.format(new Date(sup)) + " data: " + data[i]);
tmpds.addTemporalElement(
i,
inf,
sup,
granularity,
TemporalElementStore.PRIMITIVE_INTERVAL);
TemporalObject to = tmpds.addTemporalObject(i, i);
to.set(name, data[i]);
}
return tmpds;
} else if ("zoo".equals(x.asString())) {
// zoo ... feature-rich R time series class
double start = engine.parseAndEval(
"as.numeric(start(" + name + "))", null, true).asDouble();
double[] data = engine.parseAndEval("coredata(" + name + ")", null,
true).asDoubles();
double[] time = engine.parseAndEval(
"as.numeric(time(" + name + "))", null, true).asDoubles();
logger.debug("ts with start: " + start + ", obs: " + data.length);
Granularity granularity = calendar.getBottomGranularity();
// relational
TemporalDataset tmpds = new timeBench.data.TemporalDataset();
tmpds.addDataColumn(name, double.class, null);
// time indices are only used in log file to check our code
DateFormat df = null;
if (logger.isTraceEnabled()) {
df = DateFormat.getDateTimeInstance();
}
for (int i = 0; i < data.length; i++) {
long inf = Math.round(time[i] * 1000);
if (logger.isTraceEnabled())
logger.trace("time from R: " + time[i] + " inf: "
+ df.format(new Date(inf)) + " data: " + data[i]);
tmpds.addTemporalElement(
i,
inf,
inf,
granularity,
TemporalElementStore.PRIMITIVE_INSTANT);
TemporalObject to = tmpds.addTemporalObject(i, i);
to.set(name, data[i]);
}
return tmpds;
} else
throw new TemporalDataException("Unsupported R class: "
+ x.asString());
}
public void putTemporalDataset(String name,
TemporalDataset tmpds, String dataField)
throws TemporalDataException, REngineException {
double[] time = new double[tmpds.getTemporalObjectCount()];
double[] data = new double[tmpds.getTemporalObjectCount()];
int i = 0;
int dataCol = tmpds.getNodeTable().getColumnNumber(dataField);
for (TemporalObject cur : tmpds.temporalObjects()) {
if (cur.getTemporalElement().isAnchored()) {
time[i] = ((double) cur.getTemporalElement().asGeneric()
.getInf()) / 1000.0d;
data[i] = cur.getDouble(dataCol);
i++;
} else {
logger.debug("skip temp.o. with temp.el. "
+ cur.getTemporalElement());
}
}
logger.trace(i);
if (i == 0)
throw new TemporalDataException(
"TemporalDataSet did not contain any anchored objects.");
// shorten arrays, if some temp.obj. were skipped
if (i < time.length || i < data.length) {
double[] temp = new double[i];
System.arraycopy(time, 0, temp, 0, i);
time = temp;
System.arraycopy(data, 0, temp, 0, i);
data = temp;
}
engine.assign(name + ".time", time);
engine.assign(name + ".data", data);
this.exec(name + " <- zoo(" + name + ".data)");
// work around a possible timezone bug in as.POSIXct.numeric
// cp. http://stackoverflow.com/questions/2457129/converting-unix-seconds-in-milliseconds-to-posixct-posixlt
// this.exec("time(" + name + ") <- as.POSIXct(" + name +
// ".time, origin=\"1970-01-01 GMT\")");
this.exec("time(" + name + ") <- as.POSIXct(as.POSIXlt(" + name
+ ".time, origin=\"1970-01-01\"))");
}
public void putTemporalDataset(String name,
TemporalDataset tmpds, String dataField,
int startYear, int startMonth, double frequency, int length)
throws REngineException {
double[] data = new double[length];
Arrays.fill(data, REXPDouble.NA);
if (frequency != 12.0)
throw new RuntimeException("only months supported");
Granularity granularity = CalendarFactory.getSingleton().getGranularity(
JavaDateCalendarManager.getSingleton().getDefaultCalendar(),
"Month","Top");
int dataCol = tmpds.getNodeTable().getColumnNumber(dataField);
for (TemporalObject cur : tmpds.temporalObjects()) {
TemporalElement elem = cur.getTemporalElement();
if (!elem.isAnchored()) {
logger.debug("skip temp.o. with unanchored temp.el. " + elem);
} else if (elem.getGranularityId() != granularity.getIdentifier()
|| elem.getGranularityContextId() != granularity.getGranularityContextIdentifier()) {
logger.debug("skip temp.o. with wrong granularity " + elem);
} else {
long inf = elem.asGeneric().getInf();
GregorianCalendar cal = new GregorianCalendar(
TimeZone.getTimeZone("UTC"));
cal.setTimeInMillis(inf);
int year = cal.get(GregorianCalendar.YEAR);
int month = cal.get(GregorianCalendar.MONTH) + 1;
int index = (year - startYear) * 12 + month - startMonth;
if (index >= 0 && index < length) {
data[index] = cur.getDouble(dataCol);
} else {
logger.debug("skip temp.o. out of temporal bounds " + index
+ " " + elem);
}
}
}
// copy data to R and build ts object
engine.assign(name + ".data", data);
this.exec(name + " <- ts(" + name + ".data, start = c(" + startYear
+ ", " + startMonth + "), frequency = " + frequency + ")");
}
public void exec(String command) throws REngineException {
try {
logger.debug("R> " + command);
engine.parseAndEval(command, null, false);
} catch (REXPMismatchException e) {
logger.error("unexpected exception", e);
}
}
public boolean close() {
return engine.close();
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy