private String addMean(int column, String line, int start) {
   if (start == -1) {
     line += "\tNaN";
     summaryHdr += "\t" + ResultsTable.getDefaultHeading(column);
   } else {
     float[] c = column >= 0 ? rt.getColumn(column) : null;
     if (c != null) {
       ImageProcessor ip = new FloatProcessor(c.length, 1, c, null);
       if (ip == null) return line;
       ip.setRoi(start, 0, ip.getWidth() - start, 1);
       ip = ip.crop();
       ImageStatistics stats = new FloatStatistics(ip);
       if (stats == null) return line;
       line += n(stats.mean);
     } else line += "\tNaN";
     summaryHdr += "\t" + rt.getColumnHeading(column);
   }
   return line;
 }
Example #2
0
  public static void main(String[] args) {
    String mriImage = args[0];
    String outImage = args[1];
    String segArgs = args[2];
    String outTable = args[3];
    String pdxArgs = args[4];

    System.out.println("Open: " + mriImage);
    IJ.open(mriImage);
    COPD_LungSegment tjPlug = new COPD_LungSegment();
    ImagePlus cImage = IJ.getImage();
    tjPlug.setup(segArgs, cImage);
    tjPlug.run(cImage.getProcessor());
    IJ.save(cImage, outImage);
    COPD_PDxLAAx pdxPlug = new COPD_PDxLAAx();
    pdxPlug.setup("", cImage);
    pdxPlug.run(cImage.getProcessor());
    ResultsTable rt = Analyzer.getResultsTable();
    try {
      rt.saveAs(outTable);
    } catch (IOException e) {
      e.printStackTrace();
    }

    System.out.println("Results Table\n");
    String prefix = "rtout, ";

    for (int i = 0; i < ResultsTable.MAX_COLUMNS; i++) {
      if (!rt.columnExists(i)) break;
      String tempOut = rt.getColumnHeading(i);
      for (double d : rt.getColumnAsDoubles(i)) {
        tempOut += ", " + d;
      }
      System.out.println(prefix + tempOut);
    }
  }