/**
* formatCardType.
*
* @param card a {@link forge.Card} object.
* @return a {@link java.lang.String} object.
*/
public static String formatCardType(Card card) {
ArrayList<String> list = card.getType();
StringBuilder sb = new StringBuilder();
ArrayList<String> superTypes = new ArrayList<String>();
ArrayList<String> cardTypes = new ArrayList<String>();
ArrayList<String> subTypes = new ArrayList<String>();
for (String t : list) {
if (CardUtil.isASuperType(t)) superTypes.add(t);
if (CardUtil.isACardType(t)) cardTypes.add(t);
if (CardUtil.isASubType(t)) subTypes.add(t);
}
for (String type : superTypes) {
sb.append(type).append(" ");
}
for (String type : cardTypes) {
sb.append(type).append(" ");
}
if (!subTypes.isEmpty()) sb.append("- ");
for (String type : subTypes) {
sb.append(type).append(" ");
}
return sb.toString();
}
public void draw(node leaf, Graphics2D g, int px, int py) {
int lvl = leaf.getLevel();
double l = lvl;
counts[lvl]++;
double xfraq = counts[lvl] / (spacing[lvl] + 1);
double yfraq = l / depth;
int x = new Double(1600 * xfraq).intValue();
int y = new Double(1200 * yfraq).intValue() + 10;
if (leaf.getAttr() != null) {
g.drawString(leaf.getAttr(), x - 20, y);
}
if (leaf.getCrit() != null) {
g.drawString(leaf.getCrit(), x - 20, y + 10);
}
if (leaf.getResult() != null) {
g.drawString(leaf.getResult(), x - 20, y + 10);
}
g.drawLine(x, y, px, py);
// g.fillRect(x,y,20,20);
ArrayList children = leaf.getChildren();
while (!children.isEmpty()) {
draw((node) children.remove(0), g, x, y);
}
}
@Override
public Object findElement(String s) {
List<ObjectWithWeight> elements = new ArrayList<ObjectWithWeight>();
s = s.trim();
final ListIterator<Object> it = getElementIterator(0);
while (it.hasNext()) {
final ObjectWithWeight o = new ObjectWithWeight(it.next(), s, getComparator());
if (!o.weights.isEmpty()) {
elements.add(o);
}
}
ObjectWithWeight cur = null;
ArrayList<ObjectWithWeight> current = new ArrayList<ObjectWithWeight>();
for (ObjectWithWeight element : elements) {
if (cur == null) {
cur = element;
current.add(cur);
continue;
}
final int i = element.compareWith(cur);
if (i == 0) {
current.add(element);
} else if (i < 0) {
cur = element;
current.clear();
current.add(cur);
}
}
return current.isEmpty() ? null : findClosestTo(myInitialPsiElement, current);
}
/**
* Gets the list of the vnmrj users(operators) for the current unix user logged in
*
* @return the list of vnmrj users
*/
protected Object[] getOperators() {
String strUser = System.getProperty("user.name");
User user = LoginService.getDefault().getUser(strUser);
ArrayList<String> aListOperators = user.getOperators();
if (aListOperators == null || aListOperators.isEmpty())
aListOperators = new ArrayList<String>();
Collections.sort(aListOperators);
if (aListOperators.contains(strUser)) aListOperators.remove(strUser);
aListOperators.add(0, strUser);
return (aListOperators.toArray());
}
/**
* Returns the clipboard text.
*
* @return text
*/
private static String clip() {
// copy selection to clipboard
final Clipboard clip = Toolkit.getDefaultToolkit().getSystemClipboard();
final Transferable tr = clip.getContents(null);
if (tr != null) {
final ArrayList<Object> contents = BaseXLayout.contents(tr);
if (!contents.isEmpty()) return contents.get(0).toString();
} else {
Util.debug("Clipboard has no contents.");
}
return null;
}
@Nullable
private File[] getFileArray() {
ArrayList<File> result = new ArrayList<File>();
TreePath[] selectionPaths = myTree.getSelectionPaths();
if (selectionPaths != null) {
for (TreePath selectionPath : selectionPaths) {
AbstractTreeNode treeNode = (AbstractTreeNode) selectionPath.getLastPathComponent();
result.addAll(treeNode.getFiles());
}
}
if (result.isEmpty()) return null;
return result.toArray(new File[result.size()]);
}
public void trav(ArrayList nodes, node cur) {
node temp;
while (!nodes.isEmpty()) {
temp = (node) nodes.get(0);
if (temp.getLevel() - 1 == cur.getLevel()) {
nodes.remove(0);
cur.addChild(temp);
trav(nodes, temp);
} else {
return;
}
}
}
protected void restoreTree() {
Pair<ElementNode, List<ElementNode>> selection = storeSelection();
DefaultMutableTreeNode root = getRootNode();
if (!myShowClasses || myContainerNodes.isEmpty()) {
List<ParentNode> otherObjects = new ArrayList<ParentNode>();
Enumeration<ParentNode> children = getRootNodeChildren();
ParentNode newRoot =
new ParentNode(
null, new MemberChooserObjectBase(getAllContainersNodeName()), new Ref<Integer>(0));
while (children.hasMoreElements()) {
final ParentNode nextElement = children.nextElement();
if (nextElement instanceof ContainerNode) {
final ContainerNode containerNode = (ContainerNode) nextElement;
Enumeration<MemberNode> memberNodes = containerNode.children();
List<MemberNode> memberNodesList = new ArrayList<MemberNode>();
while (memberNodes.hasMoreElements()) {
memberNodesList.add(memberNodes.nextElement());
}
for (MemberNode memberNode : memberNodesList) {
newRoot.add(memberNode);
}
} else {
otherObjects.add(nextElement);
}
}
replaceChildren(root, otherObjects);
sortNode(newRoot, myComparator);
if (newRoot.children().hasMoreElements()) root.add(newRoot);
} else {
Enumeration<ParentNode> children = getRootNodeChildren();
while (children.hasMoreElements()) {
ParentNode allClassesNode = children.nextElement();
Enumeration<MemberNode> memberNodes = allClassesNode.children();
ArrayList<MemberNode> arrayList = new ArrayList<MemberNode>();
while (memberNodes.hasMoreElements()) {
arrayList.add(memberNodes.nextElement());
}
Collections.sort(arrayList, myComparator);
for (MemberNode memberNode : arrayList) {
myNodeToParentMap.get(memberNode).add(memberNode);
}
}
replaceChildren(root, myContainerNodes);
}
myTreeModel.nodeStructureChanged(root);
defaultExpandTree();
restoreSelection(selection);
}
@NotNull
public List<Pair<TaskInfo, ProgressIndicator>> getBackgroundProcesses() {
synchronized (myOriginals) {
if (myOriginals.isEmpty()) return Collections.emptyList();
List<Pair<TaskInfo, ProgressIndicator>> result =
new ArrayList<Pair<TaskInfo, ProgressIndicator>>(myOriginals.size());
for (int i = 0; i < myOriginals.size(); i++) {
result.add(Pair.<TaskInfo, ProgressIndicator>create(myInfos.get(i), myOriginals.get(i)));
}
return Collections.unmodifiableList(result);
}
}
@Nullable
private Object findClosestTo(PsiElement path, ArrayList<ObjectWithWeight> paths) {
if (path == null || myInitialPsiElement == null) {
return paths.get(0).node;
}
final Set<PsiElement> parents = getAllParents(myInitialPsiElement);
ArrayList<ObjectWithWeight> cur = new ArrayList<ObjectWithWeight>();
int max = -1;
for (ObjectWithWeight p : paths) {
final Object last = ((TreePath) p.node).getLastPathComponent();
final List<PsiElement> elements = new ArrayList<PsiElement>();
final Object object = ((DefaultMutableTreeNode) last).getUserObject();
if (object instanceof FilteringTreeStructure.FilteringNode) {
FilteringTreeStructure.FilteringNode node = (FilteringTreeStructure.FilteringNode) object;
FilteringTreeStructure.FilteringNode candidate = node;
while (node != null) {
elements.add(getPsi(node));
node = node.getParentNode();
}
final int size = ContainerUtil.intersection(parents, elements).size();
if (size == elements.size() - 1
&& size == parents.size() - (myInitialNodeIsLeaf ? 1 : 0)
&& candidate.children().isEmpty()) {
return p.node;
}
if (size > max) {
max = size;
cur.clear();
cur.add(p);
} else if (size == max) {
cur.add(p);
}
}
}
Collections.sort(
cur,
new Comparator<ObjectWithWeight>() {
@Override
public int compare(ObjectWithWeight o1, ObjectWithWeight o2) {
final int i = o1.compareWith(o2);
return i != 0
? i
: ((TreePath) o2.node).getPathCount() - ((TreePath) o1.node).getPathCount();
}
});
return cur.isEmpty() ? null : cur.get(0).node;
}
public void recreateTree() {
System.out.println("Recreating tree");
ArrayList nodes = new ArrayList();
String attr, crit, result;
int level;
node leaf;
while (!list.isEmpty()) {
if (((String) list.remove(0)).compareTo("Node") == 0) {
leaf = new node();
attr = (String) list.remove(0);
// System.out.println("ATTR:"+attr);
crit = (String) list.remove(0);
try {
level = (new Double(crit)).intValue();
crit = null;
} catch (Exception e) {
// System.out.println("crit:"+crit);
level = (new Double((String) list.remove(0))).intValue();
}
// System.out.println("lvl:"+level);
if (level > depth) {
depth = level;
}
if (((String) list.get(0)).compareTo("Node") != 0) {
result = (String) list.remove(0);
leaf.setResult(result);
}
leaf.setSplitCriteria(crit, 0);
leaf.setLevel(level);
leaf.setAttr(attr);
if (attr.compareTo("_root") == 0) {
root = leaf;
} else {
nodes.add(leaf);
}
}
}
depth++;
levelCount(nodes);
System.out.println("Linking " + nodes.size() + " tree nodes");
trav(nodes, root);
}
private void exportCharacters() {
Object[] selectedValues = herolabsCharacterList.getSelectedValues();
HeroLabPathfinderDigester dig = new HeroLabPathfinderDigester();
boolean success = true;
ArrayList<Character> notExported = new ArrayList<Character>();
for (Object object : selectedValues) {
Character character = (Character) object;
try {
if (!dig.saveCharacter(config, character)) {
notExported.add(character);
}
} catch (IOException io) {
success = false;
errorDialog(io.getMessage(), "Something bad happened:" + io.toString());
} catch (SAXException saxe) {
success = false;
errorDialog(saxe.getMessage(), "Something bad happened:" + saxe.toString());
} catch (Exception e) {
success = false;
errorDialog(e.getMessage(), "Something bad happened:" + e.toString());
}
}
if (success) {
String message =
"Successfully exported "
+ (selectedValues.length - notExported.size())
+ " out of "
+ selectedValues.length
+ " Maptools token(s).";
if (!notExported.isEmpty()) {
message +=
" "
+ notExported.size()
+ " tokens were not exported as they are not fully configured.";
// TODO: do something more useful with this collection
}
JOptionPane.showMessageDialog(panel, message);
}
}
public void setSelectedObjectsFromDB() {
this.selectingObject = true;
this.list.clearSelection();
int offsetIdx = 0;
ArrayList<Integer> selectedIndices = new ArrayList<Integer>();
for (ObjectStructure s : this.currentChannels) {
BasicDBList selectedObjects =
Core.mongoConnector.getSelectedObjects(currentNucId, s.getIdx());
if (selectedObjects != null && !selectedObjects.isEmpty()) {
for (Object o : selectedObjects) selectedIndices.add((Integer) o + offsetIdx);
}
offsetIdx += s.getObjects().length;
}
if (!selectedIndices.isEmpty()) {
int[] selectedIdx = new int[selectedIndices.size()];
for (int i = 0; i < selectedIdx.length; i++) selectedIdx[i] = selectedIndices.get(i);
this.list.setSelectedIndices(selectedIdx);
}
this.selectingObject = false;
}
public void populateObjects() {
try {
this.listModel.removeAllElements();
if (currentChannels == null) {
return;
}
this.populatingObjects = true;
ArrayList<Integer> selection = null;
if (showSelection != null && showSelection.isSelected()) selection = new ArrayList<Integer>();
int currentIdx = 0;
for (ObjectStructure ass : currentChannels) {
Object3D[] os = ass.getObjects();
if (os != null) {
Object3DGui[] osg = new Object3DGui[os.length];
for (int i = 0; i < os.length; i++) osg[i] = new Object3DGui(os[i], ass);
if (layout instanceof ObjectManagerLayout
&& currentChannels.length == 1
&& !((ObjectManagerLayout) layout).getSortKey().equals("idx"))
this.sort(((ObjectManagerLayout) layout).getSortKey(), osg, ass.getIdx());
// System.out.println("populating objects.. nb objects:"+os.length);
for (Object3DGui o3D : osg) {
this.listModel.addElement(o3D);
if (selection != null && o3D.isInSelection()) selection.add(currentIdx);
currentIdx++;
}
// if (selection!=null) System.out.println("populating objects.. selection
// size:"+selection.size());
} // else System.out.println("no objects int channel:"+ass.getChannelName());
}
if (selection != null && !selection.isEmpty()) {
int[] sel = new int[selection.size()];
int i = 0;
for (int idx : selection) sel[i++] = idx;
list.setSelectedIndices(sel);
}
} catch (Exception e) {
exceptionPrinter.print(e, "", Core.GUIMode);
}
this.populatingObjects = false;
}
private void restoreSelection(Pair<ElementNode, List<ElementNode>> pair) {
List<ElementNode> selectedNodes = pair.second;
DefaultMutableTreeNode root = getRootNode();
ArrayList<TreePath> toSelect = new ArrayList<TreePath>();
for (ElementNode node : selectedNodes) {
DefaultMutableTreeNode treeNode = (DefaultMutableTreeNode) node;
if (root.isNodeDescendant(treeNode)) {
toSelect.add(new TreePath(treeNode.getPath()));
}
}
if (!toSelect.isEmpty()) {
myTree.setSelectionPaths(toSelect.toArray(new TreePath[toSelect.size()]));
}
ElementNode leadNode = pair.first;
if (leadNode != null) {
myTree.setLeadSelectionPath(new TreePath(((DefaultMutableTreeNode) leadNode).getPath()));
}
}
public GGNimPlayer() {
super(56, 9, 12, false);
sessionID = sessionID + requestEntry("Enter a unique session ID (ASCII >3 chars):");
agent = new TcpAgent(sessionID, serverName);
agentName = requestEntry("Enter your name (ASCII >3 chars):");
initGameWindow();
addStatusBar(30);
setStatusText("Connecting to relay " + agent.getRelay() + "...");
agent.addTcpAgentListener(new MyTcpAgentAdapter());
ArrayList<String> connectList = agent.connectToRelay(agentName, 6000);
if (connectList.isEmpty()) {
setStatusText("Connection to relay failed. Terminating now...");
TcpTools.delay(3000);
System.exit(1);
}
setStatusText("Connection established. Personal name: " + connectList.get(0));
setTitle("Player's name: " + connectList.get(0));
// Game server must be up and running
if (!agent.isBridgeConnected()) {
setStatusText("Game server not found. Terminating now...");
TcpTools.delay(3000);
System.exit(1);
}
}
/**
* Returns a coefficient of the surface the VivaeObject is on or 0 if there is no surface.
*
* @param actor
*/
public float getFrictionOfSurface(VivaeObject actor) {
ArrayList<Surface> surfacesActorIsOn = new ArrayList<Surface>();
Surface srfc;
Area actArea = actor.getArea();
for (Surface surface : surfaces) {
srfc = surface;
Area actor2intersect = (Area) actArea.clone();
actor2intersect.intersect(srfc.getArea());
if (!actor2intersect.isEmpty()) {
surfacesActorIsOn.add(srfc);
}
}
if (surfacesActorIsOn.isEmpty()) {
return 0f;
}
srfc = surfacesActorIsOn.get(surfacesActorIsOn.size() - 1);
float res = srfc.getFriction();
// System.out.println("Surface = " + srfc.getClass().toString() + " has friction " +
// res);
return res;
}
@Override
public void actionPerformed(ActionEvent axnEve) {
Object obj = axnEve.getSource();
if (obj == selectAllCB) {
Boolean state;
if (selectAllCB.isSelected()) {
state = true;
deleteBut.setVisible(true);
if (Home.titlePan.getTitle().equals("Trash")) {
restoreBut.setVisible(true);
}
} else {
state = false;
deleteBut.setVisible(false);
if (Home.titlePan.getTitle().equals("Trash")) {
restoreBut.setVisible(false);
}
}
for (int i = 0; i < table.getRowCount(); i++) {
table.setValueAt(state, i, 0);
}
} else if (obj == refreshBut || obj == backBut) {
setContent(Home.titlePan.getTitle());
backBut.setVisible(false);
} else if (obj == deleteBut) {
ArrayList selectedMessages = getSelectedMessages();
if (selectedMessages.isEmpty()) {
FootPan.setMessage(FootPan.NO_SELECTION_MESSAGE);
} else {
int option =
JOptionPane.showConfirmDialog(
Home.home.homeFrame,
"Are You Sure?",
"DELETE",
JOptionPane.YES_NO_OPTION,
JOptionPane.WARNING_MESSAGE);
if (option == 0) {
Database.deleteMessages(selectedMessages, Home.titlePan.getTitle());
setContent(Home.titlePan.getTitle());
}
}
} else if (obj == restoreBut) {
ArrayList selectedMessages = getSelectedMessages();
if (selectedMessages.isEmpty()) {
FootPan.setMessage(FootPan.NO_SELECTION_MESSAGE);
} else {
int option =
JOptionPane.showConfirmDialog(
Home.home.homeFrame,
"Are You Sure?",
"RESTORE",
JOptionPane.YES_NO_OPTION,
JOptionPane.WARNING_MESSAGE);
if (option == 0) {
Database.restoreMessages(selectedMessages);
setContent(Home.titlePan.getTitle());
}
}
}
}
@Override
protected Product readProductNodesImpl() throws IOException {
final String s = getInput().toString();
final File file0 = new File(s);
final File dir = file0.getParentFile();
final S2FilenameInfo fni0 = S2FilenameInfo.create(file0.getName());
if (fni0 == null) {
throw new IOException();
}
Header metadataHeader = null;
final Map<Integer, BandInfo> fileMap = new HashMap<Integer, BandInfo>();
if (dir != null) {
File[] files =
dir.listFiles(
new FilenameFilter() {
@Override
public boolean accept(File dir, String name) {
return name.endsWith(Sentinel2ProductReaderPlugIn.JP2_EXT);
}
});
if (files != null) {
for (File file : files) {
int bandIndex = fni0.getBand(file.getName());
if (bandIndex >= 0 && bandIndex < WAVEBAND_INFOS.length) {
final S2WavebandInfo wavebandInfo = WAVEBAND_INFOS[bandIndex];
BandInfo bandInfo =
new BandInfo(
file, bandIndex, wavebandInfo, imageLayouts[wavebandInfo.resolution.id]);
fileMap.put(bandIndex, bandInfo);
}
}
}
File[] metadataFiles =
dir.listFiles(
new FilenameFilter() {
@Override
public boolean accept(File dir, String name) {
return name.startsWith("MTD_") && name.endsWith(".xml");
}
});
if (metadataFiles != null && metadataFiles.length > 0) {
File metadataFile = metadataFiles[0];
try {
metadataHeader = Header.parseHeader(metadataFile);
} catch (JDOMException e) {
BeamLogManager.getSystemLogger()
.warning("Failed to parse metadata file: " + metadataFile);
}
} else {
BeamLogManager.getSystemLogger().warning("No metadata file found");
}
}
final ArrayList<Integer> bandIndexes = new ArrayList<Integer>(fileMap.keySet());
Collections.sort(bandIndexes);
if (bandIndexes.isEmpty()) {
throw new IOException("No valid bands found.");
}
String prodType = "S2_MSI_" + fni0.procLevel;
final Product product =
new Product(
String.format("%s_%s_%s", prodType, fni0.orbitNo, fni0.tileId),
prodType,
imageLayouts[S2Resolution.R10M.id].width,
imageLayouts[S2Resolution.R10M.id].height);
try {
product.setStartTime(ProductData.UTC.parse(fni0.start, "yyyyMMddHHmmss"));
} catch (ParseException e) {
// warn
}
try {
product.setEndTime(ProductData.UTC.parse(fni0.stop, "yyyyMMddHHmmss"));
} catch (ParseException e) {
// warn
}
if (metadataHeader != null) {
SceneDescription sceneDescription = SceneDescription.create(metadataHeader);
int tileIndex = sceneDescription.getTileIndex(fni0.tileId);
Envelope2D tileEnvelope = sceneDescription.getTileEnvelope(tileIndex);
Header.Tile tile = metadataHeader.getTileList().get(tileIndex);
try {
product.setGeoCoding(
new CrsGeoCoding(
tileEnvelope.getCoordinateReferenceSystem(),
imageLayouts[S2Resolution.R10M.id].width,
imageLayouts[S2Resolution.R10M.id].height,
tile.tileGeometry10M.upperLeftX,
tile.tileGeometry10M.upperLeftY,
tile.tileGeometry10M.xDim,
-tile.tileGeometry10M.yDim,
0.0,
0.0));
} catch (FactoryException e) {
// todo - handle e
} catch (TransformException e) {
// todo - handle e
}
}
for (Integer bandIndex : bandIndexes) {
final BandInfo bandInfo = fileMap.get(bandIndex);
final Band band = product.addBand(bandInfo.wavebandInfo.bandName, ProductData.TYPE_UINT16);
band.setSpectralWavelength((float) bandInfo.wavebandInfo.centralWavelength);
band.setSpectralBandwidth((float) bandInfo.wavebandInfo.bandWidth);
band.setSpectralBandIndex(bandIndex);
band.setSourceImage(new DefaultMultiLevelImage(new Jp2MultiLevelSource(bandInfo)));
}
product.setNumResolutionLevels(imageLayouts[0].numResolutions);
return product;
}
private boolean hasProgressIndicators() {
synchronized (myOriginals) {
return !myOriginals.isEmpty();
}
}
public void build_bricks() {
ImagePlus imp;
ImagePlus orgimp;
ImageStack stack;
FileInfo finfo;
if (lvImgTitle.isEmpty()) return;
orgimp = WindowManager.getImage(lvImgTitle.get(0));
imp = orgimp;
finfo = imp.getFileInfo();
if (finfo == null) return;
int[] dims = imp.getDimensions();
int imageW = dims[0];
int imageH = dims[1];
int nCh = dims[2];
int imageD = dims[3];
int nFrame = dims[4];
int bdepth = imp.getBitDepth();
double xspc = finfo.pixelWidth;
double yspc = finfo.pixelHeight;
double zspc = finfo.pixelDepth;
double z_aspect = Math.max(xspc, yspc) / zspc;
int orgW = imageW;
int orgH = imageH;
int orgD = imageD;
double orgxspc = xspc;
double orgyspc = yspc;
double orgzspc = zspc;
lv = lvImgTitle.size();
if (filetype == "JPEG") {
for (int l = 0; l < lv; l++) {
if (WindowManager.getImage(lvImgTitle.get(l)).getBitDepth() != 8) {
IJ.error("A SOURCE IMAGE MUST BE 8BIT GLAYSCALE");
return;
}
}
}
// calculate levels
/* int baseXY = 256;
int baseZ = 256;
if (z_aspect < 0.5) baseZ = 128;
if (z_aspect > 2.0) baseXY = 128;
if (z_aspect >= 0.5 && z_aspect < 1.0) baseZ = (int)(baseZ*z_aspect);
if (z_aspect > 1.0 && z_aspect <= 2.0) baseXY = (int)(baseXY/z_aspect);
IJ.log("Z_aspect: " + z_aspect);
IJ.log("BaseXY: " + baseXY);
IJ.log("BaseZ: " + baseZ);
*/
int baseXY = 256;
int baseZ = 128;
int dbXY = Math.max(orgW, orgH) / baseXY;
if (Math.max(orgW, orgH) % baseXY > 0) dbXY *= 2;
int dbZ = orgD / baseZ;
if (orgD % baseZ > 0) dbZ *= 2;
lv = Math.max(log2(dbXY), log2(dbZ)) + 1;
int ww = orgW;
int hh = orgH;
int dd = orgD;
for (int l = 0; l < lv; l++) {
int bwnum = ww / baseXY;
if (ww % baseXY > 0) bwnum++;
int bhnum = hh / baseXY;
if (hh % baseXY > 0) bhnum++;
int bdnum = dd / baseZ;
if (dd % baseZ > 0) bdnum++;
if (bwnum % 2 == 0) bwnum++;
if (bhnum % 2 == 0) bhnum++;
if (bdnum % 2 == 0) bdnum++;
int bw = (bwnum <= 1) ? ww : ww / bwnum + 1 + (ww % bwnum > 0 ? 1 : 0);
int bh = (bhnum <= 1) ? hh : hh / bhnum + 1 + (hh % bhnum > 0 ? 1 : 0);
int bd = (bdnum <= 1) ? dd : dd / bdnum + 1 + (dd % bdnum > 0 ? 1 : 0);
bwlist.add(bw);
bhlist.add(bh);
bdlist.add(bd);
IJ.log("LEVEL: " + l);
IJ.log(" width: " + ww);
IJ.log(" hight: " + hh);
IJ.log(" depth: " + dd);
IJ.log(" bw: " + bw);
IJ.log(" bh: " + bh);
IJ.log(" bd: " + bd);
int xyl2 = Math.max(ww, hh) / baseXY;
if (Math.max(ww, hh) % baseXY > 0) xyl2 *= 2;
if (lv - 1 - log2(xyl2) <= l) {
ww /= 2;
hh /= 2;
}
IJ.log(" xyl2: " + (lv - 1 - log2(xyl2)));
int zl2 = dd / baseZ;
if (dd % baseZ > 0) zl2 *= 2;
if (lv - 1 - log2(zl2) <= l) dd /= 2;
IJ.log(" zl2: " + (lv - 1 - log2(zl2)));
if (l < lv - 1) {
lvImgTitle.add(lvImgTitle.get(0) + "_level" + (l + 1));
IJ.selectWindow(lvImgTitle.get(0));
IJ.run(
"Scale...",
"x=- y=- z=- width="
+ ww
+ " height="
+ hh
+ " depth="
+ dd
+ " interpolation=Bicubic average process create title="
+ lvImgTitle.get(l + 1));
}
}
for (int l = 0; l < lv; l++) {
IJ.log(lvImgTitle.get(l));
}
Document doc = newXMLDocument();
Element root = doc.createElement("BRK");
root.setAttribute("version", "1.0");
root.setAttribute("nLevel", String.valueOf(lv));
root.setAttribute("nChannel", String.valueOf(nCh));
root.setAttribute("nFrame", String.valueOf(nFrame));
doc.appendChild(root);
for (int l = 0; l < lv; l++) {
IJ.showProgress(0.0);
int[] dims2 = imp.getDimensions();
IJ.log(
"W: "
+ String.valueOf(dims2[0])
+ " H: "
+ String.valueOf(dims2[1])
+ " C: "
+ String.valueOf(dims2[2])
+ " D: "
+ String.valueOf(dims2[3])
+ " T: "
+ String.valueOf(dims2[4])
+ " b: "
+ String.valueOf(bdepth));
bw = bwlist.get(l).intValue();
bh = bhlist.get(l).intValue();
bd = bdlist.get(l).intValue();
boolean force_pow2 = false;
/* if(IsPowerOf2(bw) && IsPowerOf2(bh) && IsPowerOf2(bd)) force_pow2 = true;
if(force_pow2){
//force pow2
if(Pow2(bw) > bw) bw = Pow2(bw)/2;
if(Pow2(bh) > bh) bh = Pow2(bh)/2;
if(Pow2(bd) > bd) bd = Pow2(bd)/2;
}
if(bw > imageW) bw = (Pow2(imageW) == imageW) ? imageW : Pow2(imageW)/2;
if(bh > imageH) bh = (Pow2(imageH) == imageH) ? imageH : Pow2(imageH)/2;
if(bd > imageD) bd = (Pow2(imageD) == imageD) ? imageD : Pow2(imageD)/2;
*/
if (bw > imageW) bw = imageW;
if (bh > imageH) bh = imageH;
if (bd > imageD) bd = imageD;
if (bw <= 1 || bh <= 1 || bd <= 1) break;
if (filetype == "JPEG" && (bw < 8 || bh < 8)) break;
Element lvnode = doc.createElement("Level");
lvnode.setAttribute("lv", String.valueOf(l));
lvnode.setAttribute("imageW", String.valueOf(imageW));
lvnode.setAttribute("imageH", String.valueOf(imageH));
lvnode.setAttribute("imageD", String.valueOf(imageD));
lvnode.setAttribute("xspc", String.valueOf(xspc));
lvnode.setAttribute("yspc", String.valueOf(yspc));
lvnode.setAttribute("zspc", String.valueOf(zspc));
lvnode.setAttribute("bitDepth", String.valueOf(bdepth));
root.appendChild(lvnode);
Element brksnode = doc.createElement("Bricks");
brksnode.setAttribute("brick_baseW", String.valueOf(bw));
brksnode.setAttribute("brick_baseH", String.valueOf(bh));
brksnode.setAttribute("brick_baseD", String.valueOf(bd));
lvnode.appendChild(brksnode);
ArrayList<Brick> bricks = new ArrayList<Brick>();
int mw, mh, md, mw2, mh2, md2;
double tx0, ty0, tz0, tx1, ty1, tz1;
double bx0, by0, bz0, bx1, by1, bz1;
for (int k = 0; k < imageD; k += bd) {
if (k > 0) k--;
for (int j = 0; j < imageH; j += bh) {
if (j > 0) j--;
for (int i = 0; i < imageW; i += bw) {
if (i > 0) i--;
mw = Math.min(bw, imageW - i);
mh = Math.min(bh, imageH - j);
md = Math.min(bd, imageD - k);
if (force_pow2) {
mw2 = Pow2(mw);
mh2 = Pow2(mh);
md2 = Pow2(md);
} else {
mw2 = mw;
mh2 = mh;
md2 = md;
}
if (filetype == "JPEG") {
if (mw2 < 8) mw2 = 8;
if (mh2 < 8) mh2 = 8;
}
tx0 = i == 0 ? 0.0d : ((mw2 - mw + 0.5d) / mw2);
ty0 = j == 0 ? 0.0d : ((mh2 - mh + 0.5d) / mh2);
tz0 = k == 0 ? 0.0d : ((md2 - md + 0.5d) / md2);
tx1 = 1.0d - 0.5d / mw2;
if (mw < bw) tx1 = 1.0d;
if (imageW - i == bw) tx1 = 1.0d;
ty1 = 1.0d - 0.5d / mh2;
if (mh < bh) ty1 = 1.0d;
if (imageH - j == bh) ty1 = 1.0d;
tz1 = 1.0d - 0.5d / md2;
if (md < bd) tz1 = 1.0d;
if (imageD - k == bd) tz1 = 1.0d;
bx0 = i == 0 ? 0.0d : (i + 0.5d) / (double) imageW;
by0 = j == 0 ? 0.0d : (j + 0.5d) / (double) imageH;
bz0 = k == 0 ? 0.0d : (k + 0.5d) / (double) imageD;
bx1 = Math.min((i + bw - 0.5d) / (double) imageW, 1.0d);
if (imageW - i == bw) bx1 = 1.0d;
by1 = Math.min((j + bh - 0.5d) / (double) imageH, 1.0d);
if (imageH - j == bh) by1 = 1.0d;
bz1 = Math.min((k + bd - 0.5d) / (double) imageD, 1.0d);
if (imageD - k == bd) bz1 = 1.0d;
int x, y, z;
x = i - (mw2 - mw);
y = j - (mh2 - mh);
z = k - (md2 - md);
bricks.add(
new Brick(
x, y, z, mw2, mh2, md2, 0, 0, tx0, ty0, tz0, tx1, ty1, tz1, bx0, by0, bz0, bx1,
by1, bz1));
}
}
}
Element fsnode = doc.createElement("Files");
lvnode.appendChild(fsnode);
stack = imp.getStack();
int totalbricknum = nFrame * nCh * bricks.size();
int curbricknum = 0;
for (int f = 0; f < nFrame; f++) {
for (int ch = 0; ch < nCh; ch++) {
int sizelimit = bdsizelimit * 1024 * 1024;
int bytecount = 0;
int filecount = 0;
int pd_bufsize = Math.max(sizelimit, bw * bh * bd * bdepth / 8);
byte[] packed_data = new byte[pd_bufsize];
String base_dataname =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f);
String current_dataname = base_dataname + "_data" + filecount;
Brick b_first = bricks.get(0);
if (b_first.z_ != 0) IJ.log("warning");
int st_z = b_first.z_;
int ed_z = b_first.z_ + b_first.d_;
LinkedList<ImageProcessor> iplist = new LinkedList<ImageProcessor>();
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
// ImagePlus test;
// ImageStack tsst;
// test = NewImage.createByteImage("test", imageW, imageH, imageD,
// NewImage.FILL_BLACK);
// tsst = test.getStack();
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
if (ed_z > b.z_ || st_z < b.z_ + b.d_) {
if (b.z_ > st_z) {
for (int s = 0; s < b.z_ - st_z; s++) iplist.pollFirst();
st_z = b.z_;
} else if (b.z_ < st_z) {
IJ.log("warning");
for (int s = st_z - 1; s > b.z_; s--)
iplist.addFirst(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
st_z = b.z_;
}
if (b.z_ + b.d_ > ed_z) {
for (int s = ed_z; s < b.z_ + b.d_; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
ed_z = b.z_ + b.d_;
} else if (b.z_ + b.d_ < ed_z) {
IJ.log("warning");
for (int s = 0; s < ed_z - (b.z_ + b.d_); s++) iplist.pollLast();
ed_z = b.z_ + b.d_;
}
} else {
IJ.log("warning");
iplist.clear();
st_z = b.z_;
ed_z = b.z_ + b.d_;
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
}
if (iplist.size() != b.d_) {
IJ.log("Stack Error");
return;
}
// int zz = st_z;
int bsize = 0;
byte[] bdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Iterator<ImageProcessor> ipite = iplist.iterator();
while (ipite.hasNext()) {
// ImageProcessor tsip = tsst.getProcessor(zz+1);
ImageProcessor ip = ipite.next();
ip.setRoi(b.x_, b.y_, b.w_, b.h_);
if (bdepth == 8) {
byte[] data = (byte[]) ip.crop().getPixels();
System.arraycopy(data, 0, bdata, bsize, data.length);
bsize += data.length;
} else if (bdepth == 16) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
short[] data = (short[]) ip.crop().getPixels();
for (short e : data) buffer.putShort(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
} else if (bdepth == 32) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
float[] data = (float[]) ip.crop().getPixels();
for (float e : data) buffer.putFloat(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
}
}
String filename =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f)
+ "_ID"
+ String.valueOf(i);
int offset = bytecount;
int datasize = bdata.length;
if (filetype == "RAW") {
int dummy = -1;
// do nothing
}
if (filetype == "JPEG" && bdepth == 8) {
try {
DataBufferByte db = new DataBufferByte(bdata, datasize);
Raster raster = Raster.createPackedRaster(db, b.w_, b.h_ * b.d_, 8, null);
BufferedImage img =
new BufferedImage(b.w_, b.h_ * b.d_, BufferedImage.TYPE_BYTE_GRAY);
img.setData(raster);
ByteArrayOutputStream baos = new ByteArrayOutputStream();
ImageOutputStream ios = ImageIO.createImageOutputStream(baos);
String format = "jpg";
Iterator<javax.imageio.ImageWriter> iter =
ImageIO.getImageWritersByFormatName("jpeg");
javax.imageio.ImageWriter writer = iter.next();
ImageWriteParam iwp = writer.getDefaultWriteParam();
iwp.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
iwp.setCompressionQuality((float) jpeg_quality * 0.01f);
writer.setOutput(ios);
writer.write(null, new IIOImage(img, null, null), iwp);
// ImageIO.write(img, format, baos);
bdata = baos.toByteArray();
datasize = bdata.length;
} catch (IOException e) {
e.printStackTrace();
return;
}
}
if (filetype == "ZLIB") {
byte[] tmpdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Deflater compresser = new Deflater();
compresser.setInput(bdata);
compresser.setLevel(Deflater.DEFAULT_COMPRESSION);
compresser.setStrategy(Deflater.DEFAULT_STRATEGY);
compresser.finish();
datasize = compresser.deflate(tmpdata);
bdata = tmpdata;
compresser.end();
}
if (bytecount + datasize > sizelimit && bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
filecount++;
current_dataname = base_dataname + "_data" + filecount;
bytecount = 0;
offset = 0;
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
} else {
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
}
Element filenode = doc.createElement("File");
filenode.setAttribute("filename", current_dataname);
filenode.setAttribute("channel", String.valueOf(ch));
filenode.setAttribute("frame", String.valueOf(f));
filenode.setAttribute("brickID", String.valueOf(i));
filenode.setAttribute("offset", String.valueOf(offset));
filenode.setAttribute("datasize", String.valueOf(datasize));
filenode.setAttribute("filetype", String.valueOf(filetype));
fsnode.appendChild(filenode);
curbricknum++;
IJ.showProgress((double) (curbricknum) / (double) (totalbricknum));
}
if (bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
}
}
}
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
Element bricknode = doc.createElement("Brick");
bricknode.setAttribute("id", String.valueOf(i));
bricknode.setAttribute("st_x", String.valueOf(b.x_));
bricknode.setAttribute("st_y", String.valueOf(b.y_));
bricknode.setAttribute("st_z", String.valueOf(b.z_));
bricknode.setAttribute("width", String.valueOf(b.w_));
bricknode.setAttribute("height", String.valueOf(b.h_));
bricknode.setAttribute("depth", String.valueOf(b.d_));
brksnode.appendChild(bricknode);
Element tboxnode = doc.createElement("tbox");
tboxnode.setAttribute("x0", String.valueOf(b.tx0_));
tboxnode.setAttribute("y0", String.valueOf(b.ty0_));
tboxnode.setAttribute("z0", String.valueOf(b.tz0_));
tboxnode.setAttribute("x1", String.valueOf(b.tx1_));
tboxnode.setAttribute("y1", String.valueOf(b.ty1_));
tboxnode.setAttribute("z1", String.valueOf(b.tz1_));
bricknode.appendChild(tboxnode);
Element bboxnode = doc.createElement("bbox");
bboxnode.setAttribute("x0", String.valueOf(b.bx0_));
bboxnode.setAttribute("y0", String.valueOf(b.by0_));
bboxnode.setAttribute("z0", String.valueOf(b.bz0_));
bboxnode.setAttribute("x1", String.valueOf(b.bx1_));
bboxnode.setAttribute("y1", String.valueOf(b.by1_));
bboxnode.setAttribute("z1", String.valueOf(b.bz1_));
bricknode.appendChild(bboxnode);
}
if (l < lv - 1) {
imp = WindowManager.getImage(lvImgTitle.get(l + 1));
int[] newdims = imp.getDimensions();
imageW = newdims[0];
imageH = newdims[1];
imageD = newdims[3];
xspc = orgxspc * ((double) orgW / (double) imageW);
yspc = orgyspc * ((double) orgH / (double) imageH);
zspc = orgzspc * ((double) orgD / (double) imageD);
bdepth = imp.getBitDepth();
}
}
File newXMLfile = new File(directory + basename + ".vvd");
writeXML(newXMLfile, doc);
for (int l = 1; l < lv; l++) {
imp = WindowManager.getImage(lvImgTitle.get(l));
imp.changes = false;
imp.close();
}
}