public static void main(String[] args) throws Exception {
Reader trainingFile = null;
// Process arguments
int restArgs = commandOptions.processOptions(args);
// Check arguments
if (restArgs != args.length) {
commandOptions.printUsage(true);
throw new IllegalArgumentException("Unexpected arg " + args[restArgs]);
}
if (trainFileOption.value == null) {
commandOptions.printUsage(true);
throw new IllegalArgumentException("Expected --train-file FILE");
}
if (modelFileOption.value == null) {
commandOptions.printUsage(true);
throw new IllegalArgumentException("Expected --model-file FILE");
}
// Get the CRF structure specification.
ZipFile zipFile = new ZipFile(modelFileOption.value);
ZipEntry zipEntry = zipFile.getEntry("crf-info.xml");
CRFInfo crfInfo = new CRFInfo(zipFile.getInputStream(zipEntry));
StringBuffer crfInfoBuffer = new StringBuffer();
BufferedReader reader =
new BufferedReader(new InputStreamReader(zipFile.getInputStream(zipEntry)));
String line;
while ((line = reader.readLine()) != null) {
crfInfoBuffer.append(line).append('\n');
}
reader.close();
// Create the CRF, and train it.
CRF4 crf = createCRF(trainFileOption.value, crfInfo);
// Create a new zip file for our output. This will overwrite
// the file we used for input.
ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(modelFileOption.value));
// Copy the CRF info xml to the output zip file.
zos.putNextEntry(new ZipEntry("crf-info.xml"));
BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(zos));
writer.write(crfInfoBuffer.toString());
writer.flush();
zos.closeEntry();
// Save the CRF classifier model to the output zip file.
zos.putNextEntry(new ZipEntry("crf-model.ser"));
ObjectOutputStream oos = new ObjectOutputStream(zos);
oos.writeObject(crf);
oos.flush();
zos.closeEntry();
zos.close();
}
public void run() {
try {
BufferedReader br =
new BufferedReader(new InputStreamReader(new FileInputStream(file), charset));
if (outputFile != null) {
bw =
new BufferedWriter(new OutputStreamWriter(new FileOutputStream(outputFile), charset));
}
String line;
while ((line = br.readLine()) != null) {
filePosition += line.length() + 2;
line = line.trim();
if (!line.startsWith("#")) {
String[] sides = split(line);
if ((sides != null) && !sides[0].equals("key")) {
if (searchPHI) {
// Search the decrypted PHI for the searchText
sides[0] = decrypt(sides[0]);
if (sides[0].indexOf(searchText) != -1) {
output(sides[0] + " = " + sides[1] + "\n");
}
} else {
// Search the trial ID for the searchText
if (sides[1].indexOf(searchText) != -1) {
sides[0] = decrypt(sides[0]);
output(sides[0] + " = " + sides[1] + "\n");
}
}
}
}
}
br.close();
if (bw != null) {
bw.flush();
bw.close();
}
} catch (Exception e) {
append("\n\n" + e.getClass().getName() + ": " + e.getMessage() + "\n");
}
append("\nDone.\n");
setMessage("Ready...");
}
/**
* Writes the data to the given writer.
*
* @param aDataSet the project to write the settings for, cannot be <code>null</code> ;
* @param aWriter the writer to write the data to, cannot be <code>null</code>.
* @throws IOException in case of I/O problems.
*/
public static void write(final StubDataSet aDataSet, final Writer aWriter) throws IOException {
final BufferedWriter bw = new BufferedWriter(aWriter);
final AcquisitionResult capturedData = aDataSet.getCapturedData();
final Cursor[] cursors = aDataSet.getCursors();
final boolean cursorsEnabled = aDataSet.isCursorsEnabled();
try {
final int[] values = capturedData.getValues();
final long[] timestamps = capturedData.getTimestamps();
bw.write(";Size: ");
bw.write(Integer.toString(values.length));
bw.newLine();
bw.write(";Rate: ");
bw.write(Integer.toString(capturedData.getSampleRate()));
bw.newLine();
bw.write(";Channels: ");
bw.write(Integer.toString(capturedData.getChannels()));
bw.newLine();
bw.write(";EnabledChannels: ");
bw.write(Integer.toString(capturedData.getEnabledChannels()));
bw.newLine();
if (capturedData.hasTriggerData()) {
bw.write(";TriggerPosition: ");
bw.write(Long.toString(capturedData.getTriggerPosition()));
bw.newLine();
}
bw.write(";Compressed: ");
bw.write(Boolean.toString(true));
bw.newLine();
bw.write(";AbsoluteLength: ");
bw.write(Long.toString(capturedData.getAbsoluteLength()));
bw.newLine();
bw.write(";CursorEnabled: ");
bw.write(Boolean.toString(cursorsEnabled));
bw.newLine();
for (int i = 0; cursorsEnabled && (i < cursors.length); i++) {
if (cursors[i].isDefined()) {
bw.write(String.format(";Cursor%d: ", Integer.valueOf(i)));
bw.write(Long.toString(cursors[i].getTimestamp()));
bw.newLine();
}
}
for (int i = 0; i < values.length; i++) {
bw.write(formatSample(values[i], timestamps[i]));
bw.newLine();
}
} finally {
bw.flush();
}
}