public static Sequence<Object> reverseSequence(Sequence a) {
ArrayListSequence<Object> result = new ArrayListSequence<Object>();
for (int i = a.size() - 1; i > -1; i = i - 1) {
result.add(a.get(i));
}
return result;
}
public void addInstance(Instance instance) {
Sequence input = (Sequence) instance.getData();
for (int j = 0; j < input.size(); j++) {
FeatureVector fv = (FeatureVector) input.get(j);
addToken(fv);
// log.info( "token:" + j + " " + fv.toString( true ) );
}
}
public Instance pipe(Instance carrier) {
Sequence data = (Sequence) carrier.getData();
Sequence target = (Sequence) carrier.getTarget();
if (data.size() != target.size())
throw new IllegalArgumentException(
"Trying to print into SimpleTagger format, where data and target lengths do not match\n"
+ "data.length = "
+ data.size()
+ ", target.length = "
+ target.size());
int N = data.size();
if (data instanceof TokenSequence) {
throw new UnsupportedOperationException("Not yet implemented.");
} else if (data instanceof FeatureVectorSequence) {
FeatureVectorSequence fvs = (FeatureVectorSequence) data;
Alphabet dict = (fvs.size() > 0) ? fvs.getFeatureVector(0).getAlphabet() : null;
for (int i = 0; i < N; i++) {
Object label = target.get(i);
writer.print(label);
FeatureVector fv = fvs.getFeatureVector(i);
for (int loc = 0; loc < fv.numLocations(); loc++) {
writer.print(' ');
String fname = dict.lookupObject(fv.indexAtLocation(loc)).toString();
double value = fv.valueAtLocation(loc);
// if (!Maths.almostEquals(value, 1.0)) {
// throw new IllegalArgumentException ("Printing to SimpleTagger format: FeatureVector
// not binary at time slice "+i+" fv:"+fv);
// }
writer.print(fname + String.valueOf(value));
}
writer.println();
}
} else {
throw new IllegalArgumentException("Don't know how to print data of type " + data);
}
writer.println();
// writer.print(getDataAlphabet());
return carrier;
}
public Transducer.TransitionIterator transitionIterator(
Sequence inputSequence, int inputPosition, Sequence outputSequence, int outputPosition) {
if (inputPosition < 0 || outputPosition < 0)
throw new UnsupportedOperationException("Epsilon transitions not implemented.");
if (inputSequence == null)
throw new UnsupportedOperationException(
"HMMs are generative models; but this is not yet implemented.");
if (!(inputSequence instanceof FeatureSequence))
throw new UnsupportedOperationException(
"HMMs currently expect Instances to have FeatureSequence data");
return new TransitionIterator(
this,
(FeatureSequence) inputSequence,
inputPosition,
(outputSequence == null ? null : (String) outputSequence.get(outputPosition)),
hmm);
}
/**
* Command-line wrapper to train, test, or run a generic CRF-based tagger.
*
* @param args the command line arguments. Options (shell and Java quoting should be added as
* needed):
* <dl>
* <dt><code>--help</code> <em>boolean</em>
* <dd>Print this command line option usage information. Give <code>true</code> for longer
* documentation. Default is <code>false</code>.
* <dt><code>--prefix-code</code> <em>Java-code</em>
* <dd>Java code you want run before any other interpreted code. Note that the text is
* interpreted without modification, so unlike some other Java code options, you need to
* include any necessary 'new's. Default is null.
* <dt><code>--gaussian-variance</code> <em>positive-number</em>
* <dd>The Gaussian prior variance used for training. Default is 10.0.
* <dt><code>--train</code> <em>boolean</em>
* <dd>Whether to train. Default is <code>false</code>.
* <dt><code>--iterations</code> <em>positive-integer</em>
* <dd>Number of training iterations. Default is 500.
* <dt><code>--test</code> <code>lab</code> or <code>seg=</code><em>start-1</em><code>.
* </code><em>continue-1</em><code>,</code>...<code>,</code><em>start-n</em><code>.
* </code><em>continue-n</em>
* <dd>Test measuring labeling or segmentation (<em>start-i</em>, <em>continue-i</em>)
* accuracy. Default is no testing.
* <dt><code>--training-proportion</code> <em>number-between-0-and-1</em>
* <dd>Fraction of data to use for training in a random split. Default is 0.5.
* <dt><code>--model-file</code> <em>filename</em>
* <dd>The filename for reading (train/run) or saving (train) the model. Default is null.
* <dt><code>--random-seed</code> <em>integer</em>
* <dd>The random seed for randomly selecting a proportion of the instance list for training
* Default is 0.
* <dt><code>--orders</code> <em>comma-separated-integers</em>
* <dd>List of label Markov orders (main and backoff) Default is 1.
* <dt><code>--forbidden</code> <em>regular-expression</em>
* <dd>If <em>label-1</em><code>,</code><em>label-2</em> matches the expression, the
* corresponding transition is forbidden. Default is <code>\\s</code> (nothing
* forbidden).
* <dt><code>--allowed</code> <em>regular-expression</em>
* <dd>If <em>label-1</em><code>,</code><em>label-2</em> does not match the expression, the
* corresponding expression is forbidden. Default is <code>.*</code> (everything
* allowed).
* <dt><code>--default-label</code> <em>string</em>
* <dd>Label for initial context and uninteresting tokens. Default is <code>O</code>.
* <dt><code>--viterbi-output</code> <em>boolean</em>
* <dd>Print Viterbi periodically during training. Default is <code>false</code>.
* <dt><code>--fully-connected</code> <em>boolean</em>
* <dd>Include all allowed transitions, even those not in training data. Default is <code>
* true</code>.
* <dt><code>--n-best</code> <em>positive-integer</em>
* <dd>Number of answers to output when applying model. Default is 1.
* <dt><code>--include-input</code> <em>boolean</em>
* <dd>Whether to include input features when printing decoding output. Default is <code>
* false</code>.
* </dl>
* Remaining arguments:
* <ul>
* <li><em>training-data-file</em> if training
* <li><em>training-and-test-data-file</em>, if training and testing with random split
* <li><em>training-data-file</em> <em>test-data-file</em> if training and testing from
* separate files
* <li><em>test-data-file</em> if testing
* <li><em>input-data-file</em> if applying to new data (unlabeled)
* </ul>
*
* @exception Exception if an error occurs
*/
public static void main(String[] args) throws Exception {
Reader trainingFile = null, testFile = null;
InstanceList trainingData = null, testData = null;
int numEvaluations = 0;
int iterationsBetweenEvals = 16;
int restArgs = commandOptions.processOptions(args);
if (restArgs == args.length) {
commandOptions.printUsage(true);
throw new IllegalArgumentException("Missing data file(s)");
}
if (trainOption.value) {
trainingFile = new FileReader(new File(args[restArgs]));
if (testOption.value != null && restArgs < args.length - 1)
testFile = new FileReader(new File(args[restArgs + 1]));
} else testFile = new FileReader(new File(args[restArgs]));
Pipe p = null;
CRF crf = null;
TransducerEvaluator eval = null;
if (continueTrainingOption.value || !trainOption.value) {
if (modelOption.value == null) {
commandOptions.printUsage(true);
throw new IllegalArgumentException("Missing model file option");
}
ObjectInputStream s = new ObjectInputStream(new FileInputStream(modelOption.value));
crf = (CRF) s.readObject();
s.close();
p = crf.getInputPipe();
} else {
p = new SimpleTaggerSentence2FeatureVectorSequence();
p.getTargetAlphabet().lookupIndex(defaultOption.value);
}
if (trainOption.value) {
p.setTargetProcessing(true);
trainingData = new InstanceList(p);
trainingData.addThruPipe(
new LineGroupIterator(trainingFile, Pattern.compile("^\\s*$"), true));
logger.info("Number of features in training data: " + p.getDataAlphabet().size());
if (testOption.value != null) {
if (testFile != null) {
testData = new InstanceList(p);
testData.addThruPipe(new LineGroupIterator(testFile, Pattern.compile("^\\s*$"), true));
} else {
Random r = new Random(randomSeedOption.value);
InstanceList[] trainingLists =
trainingData.split(
r, new double[] {trainingFractionOption.value, 1 - trainingFractionOption.value});
trainingData = trainingLists[0];
testData = trainingLists[1];
}
}
} else if (testOption.value != null) {
p.setTargetProcessing(true);
testData = new InstanceList(p);
testData.addThruPipe(new LineGroupIterator(testFile, Pattern.compile("^\\s*$"), true));
} else {
p.setTargetProcessing(false);
testData = new InstanceList(p);
testData.addThruPipe(new LineGroupIterator(testFile, Pattern.compile("^\\s*$"), true));
}
logger.info("Number of predicates: " + p.getDataAlphabet().size());
if (testOption.value != null) {
if (testOption.value.startsWith("lab"))
eval =
new TokenAccuracyEvaluator(
new InstanceList[] {trainingData, testData}, new String[] {"Training", "Testing"});
else if (testOption.value.startsWith("seg=")) {
String[] pairs = testOption.value.substring(4).split(",");
if (pairs.length < 1) {
commandOptions.printUsage(true);
throw new IllegalArgumentException(
"Missing segment start/continue labels: " + testOption.value);
}
String startTags[] = new String[pairs.length];
String continueTags[] = new String[pairs.length];
for (int i = 0; i < pairs.length; i++) {
String[] pair = pairs[i].split("\\.");
if (pair.length != 2) {
commandOptions.printUsage(true);
throw new IllegalArgumentException(
"Incorrectly-specified segment start and end labels: " + pairs[i]);
}
startTags[i] = pair[0];
continueTags[i] = pair[1];
}
eval =
new MultiSegmentationEvaluator(
new InstanceList[] {trainingData, testData},
new String[] {"Training", "Testing"},
startTags,
continueTags);
} else {
commandOptions.printUsage(true);
throw new IllegalArgumentException("Invalid test option: " + testOption.value);
}
}
if (p.isTargetProcessing()) {
Alphabet targets = p.getTargetAlphabet();
StringBuffer buf = new StringBuffer("Labels:");
for (int i = 0; i < targets.size(); i++)
buf.append(" ").append(targets.lookupObject(i).toString());
logger.info(buf.toString());
}
if (trainOption.value) {
crf =
train(
trainingData,
testData,
eval,
ordersOption.value,
defaultOption.value,
forbiddenOption.value,
allowedOption.value,
connectedOption.value,
iterationsOption.value,
gaussianVarianceOption.value,
crf);
if (modelOption.value != null) {
ObjectOutputStream s = new ObjectOutputStream(new FileOutputStream(modelOption.value));
s.writeObject(crf);
s.close();
}
} else {
if (crf == null) {
if (modelOption.value == null) {
commandOptions.printUsage(true);
throw new IllegalArgumentException("Missing model file option");
}
ObjectInputStream s = new ObjectInputStream(new FileInputStream(modelOption.value));
crf = (CRF) s.readObject();
s.close();
}
if (eval != null) test(new NoopTransducerTrainer(crf), eval, testData);
else {
boolean includeInput = includeInputOption.value();
for (int i = 0; i < testData.size(); i++) {
Sequence input = (Sequence) testData.get(i).getData();
Sequence[] outputs = apply(crf, input, nBestOption.value);
int k = outputs.length;
boolean error = false;
for (int a = 0; a < k; a++) {
if (outputs[a].size() != input.size()) {
System.err.println("Failed to decode input sequence " + i + ", answer " + a);
error = true;
}
}
if (!error) {
for (int j = 0; j < input.size(); j++) {
StringBuffer buf = new StringBuffer();
for (int a = 0; a < k; a++) buf.append(outputs[a].get(j).toString()).append(" ");
if (includeInput) {
FeatureVector fv = (FeatureVector) input.get(j);
buf.append(fv.toString(true));
}
System.out.println(buf.toString());
}
System.out.println();
}
}
}
}
}