@Override
public synchronized List<IGroup> getGroupList() {
if (groupList.isEmpty() && (!isFakeGroup())) {
if (isAcquisitionGroup()) {
// recover file groups
File[] files = FileSystemView.getFileSystemView().getFiles(referenceFile, false);
if (files != null) {
ArrayList<File> fileList = new ArrayList<File>();
fileList.addAll(Arrays.asList(files));
Collections.sort(fileList, new FileComparator());
for (File file : fileList) {
String path = file.getAbsolutePath();
int pointIndex = path.lastIndexOf('.');
if (file.isDirectory()
|| ((pointIndex > -1) && "edf".equalsIgnoreCase(path.substring(pointIndex + 1)))) {
EdfGroup group = new EdfGroup(file);
group.setParent(this);
groupList.add(group);
}
}
fileList.clear();
}
}
// else if (itemList.isEmpty()) {
//
// }
}
ArrayList<IGroup> result = new ArrayList<IGroup>();
result.addAll(groupList);
return result;
}
private List<INode> getNodes() {
List<INode> nodes = new ArrayList<INode>();
// if (objectList.isEmpty() && groupList.isEmpty()) {
// analyzeEdfFile();
// }
for (AbstractObject object : objectList) {
nodes.add(new DefaultNode(object.getName()));
}
if (isAcquisitionGroup()) {
for (EdfGroup group : groupList) {
nodes.add(new DefaultNode(group.getShortName()));
}
}
return nodes;
}
private List<IContainer> findAllContainer(IContainer container, INode[] nodes, int level) {
List<IContainer> result = new ArrayList<IContainer>();
if (container != null) {
if (container instanceof EdfGroup) {
EdfGroup group = (EdfGroup) container;
if (nodes.length > level) {
// List current node children
if (group.isAcquisitionGroup()) {
for (EdfGroup realGroup : groupList) {
result.addAll(findAllContainer(realGroup, nodes, level));
}
}
List<INode> childs = group.getNodes();
INode current = nodes[level];
for (INode node : childs) {
if (current.matchesPartNode(node)) {
if (level < nodes.length - 1) {
result.addAll(
findAllContainer(group.getContainer(node.getName()), nodes, level + 1));
}
// Create IContainer and add it to result list
else {
result.add(group.getContainer(node.getName()));
}
}
}
}
} else {
EdfDataItem dataItem = (EdfDataItem) container;
result.add(dataItem);
}
}
return result;
}
public static void main(String[] args) {
EdfGroup group =
new EdfGroup(new File("/home/viguier/NeXusFiles/EDF/test_264/test_264_test_im_00.edf"));
group.analyzeEdfFile();
}
private void analyzeEdfFile() {
if (!analyzed) {
if (referenceFile != null) {
HashMap<String, String> headerMap = new HashMap<String, String>();
try {
FileInputStream fis = new FileInputStream(referenceFile.getAbsolutePath());
DataInputStream dis = new DataInputStream(fis);
int character = -1;
StringBuffer headerBuffer = new StringBuffer();
boolean newLine = false;
while (true) {
try {
character = dis.read();
if (character == -1) {
break;
}
headerBuffer.append((char) character);
if (character == '\n') {
newLine = true;
} else {
if ((character == '}') && newLine) {
character = dis.read();
break;
}
newLine = false;
}
} catch (IOException e) {
character = -1;
break;
}
}
if (character != -1) {
char toCheck = headerBuffer.charAt(0);
while (Character.isWhitespace(toCheck) || (toCheck == '{')) {
headerBuffer.delete(0, 1);
toCheck = headerBuffer.charAt(0);
}
toCheck = headerBuffer.charAt(headerBuffer.length() - 1);
while (Character.isWhitespace(toCheck) || (toCheck == '}')) {
headerBuffer.delete(headerBuffer.length() - 1, headerBuffer.length());
toCheck = headerBuffer.charAt(headerBuffer.length() - 1);
}
String[] lines = headerBuffer.toString().split(";");
for (String line : lines) {
int separatorIndex = line.lastIndexOf('=');
if (separatorIndex > -1) {
headerMap.put(
line.substring(0, separatorIndex).trim(),
line.substring(separatorIndex + 1).trim());
}
}
readImageFromFile(headerMap, dis);
// Cleaning keys bound to image
headerMap.remove("ByteOrder");
headerMap.remove("Dim_1");
headerMap.remove("Dim_2");
headerMap.remove("DataType");
// Avoid having another item with the same name as image item
headerMap.remove("Image");
// Other DataItems
HashMap<String, EdfGroup> subGroupMap = new HashMap<String, EdfGroup>();
for (String key : headerMap.keySet()) {
int openIndex = key.lastIndexOf('(');
int closeIndex = key.lastIndexOf(')');
if ((openIndex > -1) && (closeIndex > openIndex)) {
// Group items by name
String groupName = key.substring(openIndex + 1, closeIndex);
EdfGroup subGroup = subGroupMap.get(groupName);
if (subGroup == null) {
subGroup = new EdfGroup(null);
subGroup.setName(groupName);
subGroup.setShortName(groupName);
subGroup.setAnalyzed(true);
addSubgroup(subGroup);
subGroupMap.put(groupName, subGroup);
}
String itemName = key.substring(0, openIndex).replaceAll("=", "").trim();
subGroup.addDataItem(buildDataItem(itemName, headerMap.get(key)));
} else {
// Build simple dataItem
addDataItem(buildDataItem(key, headerMap.get(key)));
}
}
subGroupMap.clear();
headerMap.clear();
dis.close();
}
} catch (FileNotFoundException e) {
// Just ignore this case
} catch (IOException e) {
// Just ignore this case
}
}
}
analyzed = true;
}
