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;
}
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);
}
}