Exemple #1
0
  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();
  }
Exemple #2
0
    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...");
    }
Exemple #3
0
  /**
   * 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();
    }
  }