/*
-- This is a helper methid to run the morph files
*/
private static void runMorphDataSet() throws Exception {
String morph_directory =
"../../thesis-datasets/morph/"; // directory where all the morph code is stored
File d = new File(morph_directory);
// get all the files from a directory
File[] fList = d.listFiles();
List<String> dir_list = new ArrayList<String>();
for (File file : fList) {
if (file.isDirectory()) {
dir_list.add(file.getName());
}
}
for (String dir : dir_list) {
directory = morph_directory + dir + "/";
System.out.println("Running TDDD " + directory);
ReadFile.readFile(directory, fileList); // read the two files
System.out.println(fileList.get(0) + " " + fileList.get(1));
preliminaryStep(directory);
startCDC();
fileList.clear();
fileArray.clear();
hashed_File_List.clear();
}
}
/**
* Finds all files in folder and in it's sub-tree of specified depth.
*
* @param file Starting folder
* @param maxDepth Depth of the tree. If 1 - just look in the folder, no sub-folders.
* @param filter file filter.
* @return List of found files.
*/
public static List<VisorLogFile> fileTree(File file, int maxDepth, @Nullable FileFilter filter) {
if (file.isDirectory()) {
File[] files = (filter == null) ? file.listFiles() : file.listFiles(filter);
if (files == null) return Collections.emptyList();
List<VisorLogFile> res = new ArrayList<>(files.length);
for (File f : files) {
if (f.isFile() && f.length() > 0) res.add(new VisorLogFile(f));
else if (maxDepth > 1) res.addAll(fileTree(f, maxDepth - 1, filter));
}
return res;
}
return F.asList(new VisorLogFile(file));
}
static public ArrayList<File> findFilesInFolder(File folder, String extension,
boolean recurse) {
ArrayList<File> files = new ArrayList<File>();
if (folder.listFiles() == null) return files;
for (File file : folder.listFiles()) {
if (file.getName().startsWith(".")) continue; // skip hidden files
if (file.getName().endsWith("." + extension))
files.add(file);
if (recurse && file.isDirectory()) {
files.addAll(findFilesInFolder(file, extension, true));
}
}
return files;
}
public static void clearFolder(File folder) {
if (folder.exists()) {
for (File child : folder.listFiles()) {
if (child.isDirectory())
clearFolder(child);
if (!child.delete())
throw new RuntimeException("Cannot delete " + child);
}
}
}
public static boolean deleteAll(File file) {
boolean b = true;
if ((file != null) && file.exists()) {
if (file.isDirectory()) {
try {
File[] files = file.listFiles();
for (File f : files) b &= deleteAll(f);
} catch (Exception e) {
return false;
}
}
b &= file.delete();
}
return b;
}
public static Vector expandFileList(String[] files, boolean inclDirs) {
Vector v = new Vector();
if (files == null) return v;
for (int i = 0; i < files.length; i++) v.add(new File(URLDecoder.decode(files[i])));
for (int i = 0; i < v.size(); i++) {
File f = (File) v.get(i);
if (f.isDirectory()) {
File[] fs = f.listFiles();
for (int n = 0; n < fs.length; n++) v.add(fs[n]);
if (!inclDirs) {
v.remove(i);
i--;
}
}
}
return v;
}
private boolean deleteDirectory(File path) {
File[] files = path.listFiles();
for (int i = 0; i < files.length; i++) {
File f = files[i];
if (f.isFile()) {
if (!f.delete()) {
return false;
}
} else {
if (!deleteDirectory(f)) {
return false;
}
}
}
if (path.delete()) {
return true;
} else {
return false;
}
}
private void cleanup(File directory) {
// Clean up from old installations, removing or renaming files.
// Note that directory is the parent of the CTP directory
// unless the original installation was done by Bill Weadock's
// all-in-one installer for Windows.
// Get a file pointing to the CTP directory.
// This might be the current directory, or
// it might be the CTP child.
File dir;
if (directory.getName().equals("RSNA")) dir = directory;
else dir = new File(directory, "CTP");
// If CTP.jar exists in this directory, it is a really
// old CTP main file - not used anymore
File ctp = new File(dir, "CTP.jar");
if (ctp.exists()) ctp.delete();
// These are old names for the Launcher.jar file
File launcher = new File(dir, "CTP-launcher.jar");
if (launcher.exists()) launcher.delete();
launcher = new File(dir, "TFS-launcher.jar");
if (launcher.exists()) launcher.delete();
// Delete the obsolete CTP-runner.jar file
File runner = new File(dir, "CTP-runner.jar");
if (runner.exists()) runner.delete();
// Delete the obsolete MIRC-copier.jar file
File copier = new File(dir, "MIRC-copier.jar");
if (copier.exists()) copier.delete();
// Rename the old versions of the properties files
File oldprops = new File(dir, "CTP-startup.properties");
File newprops = new File(dir, "CTP-launcher.properties");
File correctprops = new File(dir, "Launcher.properties");
if (oldprops.exists()) {
if (newprops.exists() || correctprops.exists()) oldprops.delete();
else oldprops.renameTo(correctprops);
}
if (newprops.exists()) {
if (correctprops.exists()) newprops.delete();
else newprops.renameTo(correctprops);
}
// Get rid of obsolete startup and shutdown programs
File startup = new File(dir, "CTP-startup.jar");
if (startup.exists()) startup.delete();
File shutdown = new File(dir, "CTP-shutdown.jar");
if (shutdown.exists()) shutdown.delete();
// Get rid of the obsolete linux directory
File linux = new File(dir, "linux");
if (linux.exists()) {
startup = new File(linux, "CTP-startup.jar");
if (startup.exists()) startup.delete();
shutdown = new File(linux, "CTP-shutdown.jar");
if (shutdown.exists()) shutdown.delete();
linux.delete();
}
// clean up the libraries directory
File libraries = new File(dir, "libraries");
if (libraries.exists()) {
// remove obsolete versions of the slf4j libraries
// and the dcm4che-imageio libraries
File[] files = libraries.listFiles();
for (File file : files) {
if (file.isFile()) {
String name = file.getName();
if (name.startsWith("slf4j-") || name.startsWith("dcm4che-imageio-rle")) {
file.delete();
}
}
}
// remove the email subdirectory
File email = new File(libraries, "email");
deleteAll(email);
// remove the xml subdirectory
File xml = new File(libraries, "xml");
deleteAll(xml);
// remove the sftp subdirectory
File sftp = new File(libraries, "sftp");
deleteAll(xml);
// move edtftpj.jar to the ftp directory
File edtftpj = new File(libraries, "edtftpj.jar");
if (edtftpj.exists()) {
File ftp = new File(libraries, "ftp");
ftp.mkdirs();
File ftpedtftpj = new File(ftp, "edtftpj.jar");
edtftpj.renameTo(ftpedtftpj);
}
}
// remove the obsolete xml library under dir
File xml = new File(dir, "xml");
deleteAll(xml);
// remove the dicom profiles so any
// obsolete files will disappear
File profiles = new File(dir, "profiles");
File dicom = new File(profiles, "dicom");
deleteAll(dicom);
dicom.mkdirs();
// Remove the index.html file so it will be rebuilt from
// example-index.html when the system next starts.
File root = new File(dir, "ROOT");
if (root.exists()) {
File index = new File(root, "index.html");
index.delete();
}
}
private File getFile(File dir, String nameStart, String nameEnd) {
File[] files = dir.listFiles(new NameFilter(nameStart, nameEnd));
if (files.length == 0) return null;
return files[0];
}
public static void deleteDirectory(File f) throws IOException {
if (f.isDirectory()) {
for (File c : f.listFiles()) deleteDirectory(c);
}
if (!f.delete()) throw new FileNotFoundException("Failed to delete file: " + f);
}