private void CopyAllFiles(String csvFilename) throws IOException, NoSuchAlgorithmException {
ResultsTable table = ResultsTable.open(csvFilename);
int size = table.getCounter();
for (int i = 0; i < size; i++) {
String source = table.getStringValue("OriginaFile", i);
String destination = table.getStringValue("WorkingFile", i);
print(i + 1 + " Move from: " + source + " to ------> " + destination);
// print("to ------> " + destination);
// imp = new ImagePlus(source);
// IJ.save(imp, destination);
CopyFile(source, destination);
StringBuffer sb1 = CheckSum(source);
StringBuffer sb2 = CheckSum(destination);
// CheckSum(source);
// check SHA1
writeChecksum(sb1, sb2, table, i);
}
table.saveAs(csvFilename);
}
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);
}
}