/**
* Returns the specified filename or "OutputFileObject" if the file OutputPort is connected.
*
* @return
* @throws OperatorException
*/
public String getSelectedFileDescription() throws OperatorException {
if (!fileOutputPort.isConnected()) {
return operator.getParameterAsString(fileParameterName);
} else {
return "OutputFileObject";
}
}
/**
* Moves the operators from this process to another process, keeping all connections intact. TODO:
* Test more rigorously. Do we register/unregister everything correctly?
*
* @return the number of ports the connections of which could not be restored
*/
public int stealOperatorsFrom(ExecutionUnit otherUnit) {
int failedReconnects = 0;
// remember source and sink connections so we can reconnect them later.
Map<String, InputPort> sourceMap = new HashMap<String, InputPort>();
Map<String, OutputPort> sinkMap = new HashMap<String, OutputPort>();
for (OutputPort source : otherUnit.getInnerSources().getAllPorts()) {
if (source.isConnected()) {
sourceMap.put(source.getName(), source.getDestination());
}
}
otherUnit.getInnerSources().disconnectAll();
for (InputPort sink : otherUnit.getInnerSinks().getAllPorts()) {
if (sink.isConnected()) {
sinkMap.put(sink.getName(), sink.getSource());
}
}
otherUnit.getInnerSinks().disconnectAll();
// Move operators
Iterator<Operator> i = otherUnit.operators.iterator();
while (i.hasNext()) {
Operator operator = i.next();
i.remove();
otherUnit.unregister(operator);
Process otherProcess = operator.getProcess();
if (otherProcess != null) {
operator.unregisterOperator(otherProcess);
}
this.operators.add(operator);
operator.setEnclosingProcess(null);
// operator.unregisterOperator(operator.getProcess());
registerOperator(operator, true);
// operator.registerOperator(this.getEnclosingOperator().getProcess());
}
// Rewire sources and sinks
for (Map.Entry<String, InputPort> entry : sourceMap.entrySet()) {
OutputPort mySource = getInnerSources().getPortByName(entry.getKey());
if (mySource != null) {
mySource.connectTo(entry.getValue());
} else {
failedReconnects++;
}
}
getInnerSources().unlockPortExtenders();
for (Map.Entry<String, OutputPort> entry : sinkMap.entrySet()) {
InputPort mySink = getInnerSinks().getPortByName(entry.getKey());
if (mySink != null) {
entry.getValue().connectTo(mySink);
} else {
failedReconnects++;
}
}
getInnerSinks().unlockPortExtenders();
fireUpdate(this);
return failedReconnects;
}
@Override
public final void doWork() throws OperatorException {
ExampleSet inputExampleSet = exampleSetInput.getData(ExampleSet.class);
ExampleSet applySet = null;
// check for needed copy of original exampleset
if (originalOutput.isConnected() && writesIntoExistingData()) {
int type = DataRowFactory.TYPE_DOUBLE_ARRAY;
if (inputExampleSet.getExampleTable() instanceof MemoryExampleTable) {
DataRowReader dataRowReader = inputExampleSet.getExampleTable().getDataRowReader();
if (dataRowReader.hasNext()) {
type = dataRowReader.next().getType();
}
}
// check if type is supported to be copied
if (type >= 0) {
applySet = MaterializeDataInMemory.materializeExampleSet(inputExampleSet, type);
}
}
if (applySet == null) applySet = (ExampleSet) inputExampleSet.clone();
// we apply on the materialized data, because writing can't take place in views anyway.
ExampleSet result = apply(applySet);
originalOutput.deliver(inputExampleSet);
exampleSetOutput.deliver(result);
}
private void addReadyOutputs(LinkedList<OutputPort> readyOutputs, OutputPorts ports) {
// add the parameters in a stack-like fashion like in pre-5.0
// Iterator<OutputPort> i = ports.getAllPorts().iterator();
Iterator<OutputPort> i = new LinkedList<OutputPort>(ports.getAllPorts()).descendingIterator();
while (i.hasNext()) {
OutputPort port = i.next();
if (!port.isConnected() && port.shouldAutoConnect()) {
readyOutputs.addLast(port);
}
}
}
/**
* Same as {@link #getSelectedFile()}, but returns true if file is specified (in the respective
* way).
*/
public boolean isFileSpecified() {
if (!fileOutputPort.isConnected()) {
return operator.isParameterSet(fileParameterName);
} else {
try {
return (fileOutputPort.getData(IOObject.class) instanceof FileObject);
} catch (OperatorException e) {
return false;
}
}
}
@Override
public void doWork() throws OperatorException {
ExampleSet exampleSet = exampleSetInput.getData(ExampleSet.class);
// only use numeric attributes
Tools.onlyNumericalAttributes(exampleSet, "KernelPCA");
Tools.onlyNonMissingValues(exampleSet, getOperatorClassName(), this);
Attributes attributes = exampleSet.getAttributes();
int numberOfExamples = exampleSet.size();
// calculating means for later zero centering
exampleSet.recalculateAllAttributeStatistics();
double[] means = new double[exampleSet.getAttributes().size()];
int i = 0;
for (Attribute attribute : exampleSet.getAttributes()) {
means[i] = exampleSet.getStatistics(attribute, Statistics.AVERAGE);
i++;
}
// kernel
Kernel kernel = Kernel.createKernel(this);
// copying zero centered exampleValues
ArrayList<double[]> exampleValues = new ArrayList<double[]>(numberOfExamples);
i = 0;
for (Example columnExample : exampleSet) {
double[] columnValues = getAttributeValues(columnExample, attributes, means);
exampleValues.add(columnValues);
i++;
}
// filling kernel matrix
Matrix kernelMatrix = new Matrix(numberOfExamples, numberOfExamples);
for (i = 0; i < numberOfExamples; i++) {
for (int j = 0; j < numberOfExamples; j++) {
kernelMatrix.set(
i, j, kernel.calculateDistance(exampleValues.get(i), exampleValues.get(j)));
}
}
// calculating eigenVectors
EigenvalueDecomposition eig = kernelMatrix.eig();
Model model = new KernelPCAModel(exampleSet, means, eig.getV(), exampleValues, kernel);
if (exampleSetOutput.isConnected()) {
exampleSetOutput.deliver(model.apply(exampleSet));
}
originalOutput.deliver(exampleSet);
modelOutput.deliver(model);
}
/**
* Returns an OutputStream, depending on whether the {@link #fileOutputPort} is connected, a file
* name is given and it should be appended to the end of the file.
*/
public OutputStream openSelectedFile(boolean append) throws OperatorException {
if (!fileOutputPort.isConnected()) {
try {
return new FileOutputStream(operator.getParameterAsFile(fileParameterName, true), append);
} catch (FileNotFoundException e) {
throw new UserError(
operator, e, 303, operator.getParameterAsFile(fileParameterName), e.getMessage());
}
} else {
return new ByteArrayOutputStream() {
@Override
public void close() throws IOException {
super.close();
fileOutputPort.deliver(new BufferedFileObject(this.toByteArray()));
}
};
}
}
private void cloneConnections(
OutputPorts originalPorts,
ExecutionUnit originalExecutionUnit,
Map<String, Operator> clonedOperatorsByName) {
for (OutputPort originalSource : originalPorts.getAllPorts()) {
if (originalSource.isConnected()) {
OutputPort mySource;
if (originalPorts.getOwner().getOperator()
== originalExecutionUnit.getEnclosingOperator()) {
// this is an inner source
mySource = getInnerSources().getPortByName(originalSource.getName());
if (mySource == null) {
throw new RuntimeException(
"Error during clone: Corresponding source for "
+ originalSource
+ " not found (no such inner source).");
}
} else {
// this is an output port
Operator myOperator =
clonedOperatorsByName.get(
originalSource.getPorts().getOwner().getOperator().getName());
if (myOperator == null) {
throw new RuntimeException(
"Error during clone: Corresponding source for "
+ originalSource
+ " not found (no such operator).");
}
mySource = myOperator.getOutputPorts().getPortByName(originalSource.getName());
if (mySource == null) {
throw new RuntimeException(
"Error during clone: Corresponding source for "
+ originalSource
+ " not found (no such output port).");
}
}
InputPort originalDestination = originalSource.getDestination();
InputPort myDestination;
if (originalDestination.getPorts().getOwner().getOperator()
== originalExecutionUnit.getEnclosingOperator()) {
// this is an inner sink
myDestination = getInnerSinks().getPortByName(originalDestination.getName());
if (myDestination == null) {
throw new RuntimeException(
"Error during clone: Corresponding destination for "
+ originalDestination
+ " not found (no such inner sink).");
}
} else {
// this is an input port
Operator myOperator =
clonedOperatorsByName.get(
originalDestination.getPorts().getOwner().getOperator().getName());
if (myOperator == null) {
throw new RuntimeException(
"Error during clone: Corresponding destination for "
+ originalDestination
+ " not found (no such operator).");
}
myDestination = myOperator.getInputPorts().getPortByName(originalDestination.getName());
if (myDestination == null) {
throw new RuntimeException(
"Error during clone: Corresponding destination for "
+ originalDestination
+ " not found (no such input port).");
}
}
mySource.connectTo(myDestination);
}
}
}
@Override
public void doWork() throws OperatorException {
String command = getParameterAsString(PARAMETER_COMMAND);
final boolean logOut = !stdout.isConnected() && getParameterAsBoolean(PARAMETER_LOG_STDOUT);
final boolean logErr = !stderr.isConnected() && getParameterAsBoolean(PARAMETER_LOG_STDERR);
final List<Throwable> exceptions = Collections.synchronizedList(new ArrayList<Throwable>(3));
try {
final Process process = Runtime.getRuntime().exec(command);
final ByteArrayOutputStream stdOutBuf = new ByteArrayOutputStream();
final ByteArrayOutputStream stdErrBuf = new ByteArrayOutputStream();
if (stdin.isConnected()) {
final FileObject input = stdin.getData(FileObject.class);
new Thread(getName() + "-stdin") {
public void run() {
try {
Tools.copyStreamSynchronously(input.openStream(), process.getOutputStream(), true);
} catch (Exception e) {
exceptions.add(e);
}
};
}.start();
}
new Thread(getName() + "-stdout") {
public void run() {
try {
if (logOut) {
logOutput("stdout:", process.getInputStream());
} else {
Tools.copyStreamSynchronously(process.getInputStream(), stdOutBuf, true);
}
} catch (Exception e) {
exceptions.add(e);
}
}
}.start();
new Thread(getName() + "-stderr") {
public void run() {
try {
if (logErr) {
logOutput("stderr:", process.getErrorStream());
} else {
Tools.copyStreamSynchronously(process.getErrorStream(), stdErrBuf, true);
}
} catch (Exception e) {
exceptions.add(e);
}
}
}.start();
Tools.waitForProcess(this, process, command);
getLogger().info("Program exited succesfully.");
if (stdout.isConnected()) {
stdout.deliver(new BufferedFileObject(stdOutBuf.toByteArray()));
}
if (stderr.isConnected()) {
stderr.deliver(new BufferedFileObject(stdErrBuf.toByteArray()));
}
} catch (IOException e) {
throw new UserError(this, e, 310, new Object[] {command, e.getMessage()});
} finally {
getLogger()
.log(
Level.WARNING,
"com.rapidminer.operator.CommandLineOperator.errors_occurred",
new Object[] {exceptions.size(), command});
for (Throwable t : exceptions) {
getLogger().log(Level.WARNING, t.toString(), t);
}
if (!exceptions.isEmpty()) {
Throwable t = exceptions.get(0);
if (t instanceof OperatorException) {
throw (OperatorException) t;
} else {
throw new UserError(this, t, 310, new Object[] {command, t.getMessage()});
}
}
}
dummyPorts.passDataThrough();
}
