public ArrayList<String> collectLinks(String p) {
ArrayList<String> PageLinks = new ArrayList<String>();
try {
URL url = new URL(p);
BufferedReader br3 = new BufferedReader(new InputStreamReader(url.openStream()));
String str = "";
while (null != (str = br3.readLine())) {
Pattern link =
Pattern.compile(
"<a target=\"_top\" href=\"/m/.*", Pattern.CASE_INSENSITIVE | Pattern.DOTALL);
Matcher match = link.matcher(str);
while (match.find()) {
String tmp = match.group();
int start = tmp.indexOf('/');
tmp = tmp.substring(start + 1, tmp.indexOf('\"', start + 1));
if (Crawl.contains("http://www.rottentomatoes.com/" + tmp)
|| ToCrawl.contains("http://www.rottentomatoes.com/" + tmp)
|| PageLinks.contains("http://www.rottentomatoes.com/" + tmp)) continue;
PageLinks.add("http://www.rottentomatoes.com/" + tmp);
// bw4.write("http://www.rottentomatoes.com/"+tmp+"\r\n");
}
}
br3.close();
} catch (Exception ex) {
ex.printStackTrace();
}
return PageLinks;
}
public void flipLayoutLeftRight() {
LayoutBox box = getExactLayoutBox();
Iterator<NodeLayout> ne = nodes.iterator();
while (ne.hasNext()) {
NodeLayout nl = ne.next();
if (nl.processID.equals("null")) {
nl.x =
box.topleft.x
+ (box.width - (nl.x - box.topleft.x))
- 60; // minus 60 which is the width of process node's box, since using upperleft
// coor
} else if (isSecondary(nl)) {
nl.x = box.topleft.x + (box.width - (nl.x - box.topleft.x)) - 60;
} else {
nl.x = box.topleft.x + (box.width - (nl.x - box.topleft.x)) - 20;
}
}
Iterator<EdgeLayout> e2 = edges.iterator();
EdgeLayout el;
while (e2.hasNext()) {
el = e2.next();
for (LayoutPoint lp : el.bends) {
lp.x = box.topleft.x + (box.width - (lp.x - box.topleft.x));
}
}
}
// convert coordinates to relative coordinates with the top-left one as (0,0)
public void convertToRelativePositions() {
LayoutBox box = getExactLayoutBox();
// System.out.println("Box
// ("+box.topleft.x+","+box.topleft.y+");("+(box.topleft.x+box.width)+","+(box.topleft.y+box.height));
Iterator<NodeLayout> e = nodes.iterator();
NodeLayout nl;
while (e.hasNext()) {
nl = e.next();
/* Debug code
if(nl.x<box.topleft.x || nl.y<box.topleft.y || nl.x>(box.topleft.x+box.width) || nl.y>(box.topleft.y+box.height)){
System.out.println("Invalid node "+nl.x+","+nl.y);
}
//*/
nl.x = nl.x - box.topleft.x;
nl.y = nl.y - box.topleft.y;
}
Iterator<EdgeLayout> e2 = edges.iterator();
EdgeLayout el;
while (e2.hasNext()) {
el = e2.next();
for (LayoutPoint lp : el.bends) {
lp.x = lp.x - box.topleft.x;
lp.y = lp.y - box.topleft.y;
}
}
}
/**
* @return exact rectangle box bounding all the center points of the nodes and all the bend
* points.
*/
public LayoutBox getExactLayoutBox() {
Iterator<NodeLayout> e = nodes.iterator();
double tlx = 0, tly = 0, brx = 0, bry = 0; // top left, bottom right
NodeLayout nl;
if (e.hasNext()) {
nl = e.next();
tlx = nl.x;
tly = nl.y;
brx = nl.x;
bry = nl.y;
}
while (e.hasNext()) {
nl = e.next();
if (nl.x < tlx) {
tlx = nl.x;
}
if (nl.x > brx) {
brx = nl.x;
}
if (nl.y < tly) {
tly = nl.y;
}
if (nl.y > bry) {
bry = nl.y;
}
}
Iterator<EdgeLayout> ee = edges.iterator();
Iterator<LayoutPoint> be;
LayoutPoint lp;
EdgeLayout el;
while (ee.hasNext()) {
el = ee.next();
be = el.bends.iterator();
while (be.hasNext()) {
lp = be.next();
if (lp.x < tlx) {
tlx = lp.x;
}
if (lp.x > brx) {
brx = lp.x;
}
if (lp.y < tly) {
tly = lp.y;
}
if (lp.y > bry) {
bry = lp.y;
}
}
}
return new LayoutBox(tlx, tly, brx - tlx, bry - tly);
}
public String toString() {
if (isEmpty()) {
return "";
}
StringBuffer sb = new StringBuffer();
Iterator<NodeLayout> e = nodes.iterator();
while (e.hasNext()) sb.append((e.next()).toString());
sb.append("\n");
Iterator<EdgeLayout> ee = edges.iterator();
while (ee.hasNext()) sb.append((ee.next()).toString());
return sb.toString();
}
/** Generates array of XContour from local contours and modules. Used for TTF building. */
private XContour[] toContours() {
XContour[] retval;
ArrayList<XContour> list = new ArrayList<>();
XContour[] contours = m_glyph.getBody().getContour();
for (int i = 0; i < contours.length; i++) {
EContour contour = (EContour) contours[i];
list.add(contour.toQuadratic());
} // for i
XModule[] modules = m_glyph.getBody().getModule();
for (int i = 0; i < modules.length; i++) {
EModuleInvoke module = (EModuleInvoke) modules[i];
// push and pop happens inside toContour
list.add(module.toContour(new AffineTransform()));
} // for i
if (list.size() == 0) return null;
retval = new XContour[list.size()];
for (int i = 0; i < list.size(); i++) {
retval[i] = list.get(i);
} // for i
return retval;
}
public String toBeautifiedString() {
StringBuffer sb = new StringBuffer();
Iterator<NodeLayout> e = nodes.iterator();
while (e.hasNext()) sb.append((e.next()).toBeautifiedString());
sb.append("\n");
Iterator<EdgeLayout> ee = edges.iterator();
while (ee.hasNext()) {
sb.append((ee.next()).toBeautifiedString());
}
sb.append("\n\nNumber of Nodes: ");
sb.append(nodes.size());
sb.append("\nNumber of Edges: ");
sb.append(edges.size() + "\n");
return sb.toString();
}
public TTGlyph toSimpleGlyph() {
// convert the file into array of contours
XContour[] contours = toContours();
if ((contours == null) && (!isRequiredGlyph())) {
return null;
} // if
TTGlyph retval = new TTGlyph();
retval.setSimple(true);
retval.setAdvanceWidth(getAdvanceWidth());
if (contours == null) {
return retval;
} // if
ArrayList<EContourPoint> points = new ArrayList<>();
for (int i = 0; i < contours.length; i++) {
XContour contour = contours[i];
XContourPoint[] contourPoints = contour.getContourPoint();
for (int j = 0; j < contourPoints.length; j++) {
points.add((EContourPoint) contourPoints[j]);
} // for j
retval.addEndPoint(points.size() - 1);
} // for i
for (EContourPoint point : points) {
loadContourPoint(retval, point);
} // for point
boolean hasGridfit = false;
// I need int i here.
for (int i = 0; i < points.size(); i++) {
EContourPoint point = points.get(i);
if (!point.isRounded()) {
continue;
} // if
hasGridfit = true;
loadGridfit(retval, point, i);
} // for i
if (hasGridfit) {
retval.addInstruction(TTGlyph.IUP1);
retval.addInstruction(TTGlyph.IUP0);
} // if
// I need int i here.
for (int i = 0; i < points.size(); i++) {
EContourPoint point = points.get(i);
if (point.getHint().length == 0) {
continue;
} // if
loadHint(retval, point, i);
} // for i
return retval;
}
public EdgeLayout getEdgeLayouts(String spid, String sid, String tpid, String tid) {
Iterator<EdgeLayout> ee = edges.iterator();
EdgeLayout el;
while (ee.hasNext()) {
el = ee.next();
if (el.sourceNode.equals(sid) && el.targetNode.equals(tid)) {
return el;
}
}
return null;
} // */
// convert coordinates to shifted coordinates with the top-left one as (xs,ys)
public void convertToShiftedPositions(double xs, double ys) {
convertToRelativePositions();
Iterator<NodeLayout> e = nodes.iterator();
NodeLayout nl;
while (e.hasNext()) {
nl = e.next();
nl.x += xs;
nl.y += ys;
}
Iterator<EdgeLayout> e2 = edges.iterator();
EdgeLayout el;
while (e2.hasNext()) {
el = e2.next();
for (LayoutPoint lp : el.bends) {
lp.x += xs;
lp.y += ys;
}
}
}
public boolean addNodeLayout(String pid, String id, String c, double x, double y) {
/*if(idToNode.containsKey(pid + id)){
return false;
} */
NodeLayout newNode = new NodeLayout(pid, id, c, x, y);
nodes.add(newNode);
idToNode.put(pid + id, newNode);
return true;
}
public void filpLayoutUpDown() {
LayoutBox box = getExactLayoutBox();
Iterator<NodeLayout> ne = nodes.iterator();
while (ne.hasNext()) {
NodeLayout nl = ne.next();
if (nl.cofactor.equalsIgnoreCase("true")) {
nl.y = box.topleft.y + (box.height - (nl.y - box.topleft.y)) - 12;
} else {
nl.y = box.topleft.y + (box.height - (nl.y - box.topleft.y)) - 20;
}
}
Iterator<EdgeLayout> e2 = edges.iterator();
EdgeLayout el;
while (e2.hasNext()) {
el = e2.next();
for (LayoutPoint lp : el.bends) {
lp.y = box.topleft.y + (box.height - (lp.y - box.topleft.y));
}
}
}
public void flipLayoutUpDown() {
LayoutBox box = getExactLayoutBox();
Iterator<NodeLayout> ne = nodes.iterator();
while (ne.hasNext()) {
NodeLayout nl = ne.next();
if (isSecondary(nl)) {
nl.y = box.topleft.y + (box.height - (nl.y - box.topleft.y)) - 12;
} else {
nl.y = box.topleft.y + (box.height - (nl.y - box.topleft.y)) - 20;
}
}
Iterator<EdgeLayout> e2 = edges.iterator();
EdgeLayout el;
while (e2.hasNext()) {
el = e2.next();
for (LayoutPoint lp : el.bends) {
lp.y = box.topleft.y + (box.height - (lp.y - box.topleft.y));
}
}
}
public String toString() {
StringBuffer sb = new StringBuffer();
sb.append(sourcepid + "," + sourceNode + "," + targetpid + "," + targetNode + ",");
Iterator<LayoutPoint> e = bends.iterator();
LayoutPoint b;
while (e.hasNext()) {
b = (LayoutPoint) e.next();
sb.append(b.x + "," + b.y + ",");
}
sb.append("\n");
return sb.toString();
}
public LayoutInfo copyOfThisLayoutInfo() {
LayoutInfo copyI = new LayoutInfo();
for (NodeLayout nl : nodes) {
copyI.addNodeLayout(nl.processID, nl.nodeID, nl.cofactor, nl.x, nl.y);
}
for (EdgeLayout el : edges) {
ArrayList<LayoutPoint> copyBends = new ArrayList<LayoutPoint>();
for (LayoutPoint lp : el.bends) {
copyBends.add(new LayoutPoint(lp.x, lp.y));
}
copyI.addEdgeLayout(
el.sourcepid,
el.sourceNode,
el.scofactor,
el.targetpid,
el.targetNode,
el.tcofactor,
copyBends);
}
return copyI;
}
public Command executeStep(Element stepRow) throws Exception {
Command command = new Command();
NodeList stepFields = stepRow.getElementsByTagName("td");
String cmd = stepFields.item(0).getTextContent().trim();
command.cmd = cmd;
ArrayList<String> argList = new ArrayList<String>();
if (stepFields.getLength() == 1) {
// skip comments
command.result = "OK";
return command;
}
for (int i = 1; i < stepFields.getLength(); i++) {
String content = stepFields.item(i).getTextContent();
content = content.replaceAll(" +", " ");
content = content.replace('\u00A0', ' ');
content = content.trim();
argList.add(content);
}
String args[] = argList.toArray(new String[0]);
command.args = args;
if (this.verbose) {
System.out.println(cmd + " " + Arrays.asList(args));
}
try {
command.result = this.commandProcessor.doCommand(cmd, args);
command.error = false;
} catch (Exception e) {
command.result = e.getMessage();
command.error = true;
}
command.failure = command.error && !cmd.startsWith("verify");
if (this.verbose) {
System.out.println(command.result);
}
return command;
}
public String toBeautifiedString() {
StringBuffer sb = new StringBuffer();
sb.append("sourcePID: " + sourcepid);
sb.append(" sourceNodeId: " + sourceNode + "\n");
sb.append(" targetPID: " + targetpid);
sb.append(" targetNodeId: " + targetNode + "\n");
Iterator<LayoutPoint> e = bends.iterator();
LayoutPoint b;
while (e.hasNext()) {
b = (LayoutPoint) e.next();
sb.append(" Bend Points: " + b.x + "," + b.y + " ");
}
sb.append("\n\n");
return sb.toString();
}
private boolean showDialog() {
String[] types = {"RAW", "JPEG", "ZLIB"};
GenericDialog gd = new GenericDialog("Generate Bricks");
gd.addChoice("FileType", types, filetype);
gd.addNumericField("JPEG quality", jpeg_quality, 0);
gd.addNumericField("Max file size (MB)", bdsizelimit, 0);
int[] wlist = WindowManager.getIDList();
if (wlist == null) return false;
String[] titles = new String[wlist.length];
for (int i = 0; i < wlist.length; i++) titles[i] = "";
int tnum = 0;
for (int i = 0; i < wlist.length; i++) {
ImagePlus imp = WindowManager.getImage(wlist[i]);
if (imp != null) {
titles[tnum] = imp.getTitle();
tnum++;
}
}
gd.addChoice("Source image: ", titles, titles[0]);
gd.showDialog();
if (gd.wasCanceled()) return false;
filetype = types[gd.getNextChoiceIndex()];
jpeg_quality = (int) gd.getNextNumber();
if (jpeg_quality > 100) jpeg_quality = 100;
if (jpeg_quality < 0) jpeg_quality = 0;
bdsizelimit = (int) gd.getNextNumber();
int id = gd.getNextChoiceIndex();
lvImgTitle = new ArrayList<String>();
lvImgTitle.add(titles[id]);
Prefs.set("filetype.string", filetype);
Prefs.set("jpeg_quality.int", jpeg_quality);
Prefs.set("bdsizelimit.int", bdsizelimit);
return true;
}
// Return the shared nodes(with the same node id) with the other LayoutInfo
public LinkedHashMap<NodeLayout, NodeLayout> sharedNodes(LayoutInfo info2) {
LinkedHashMap<NodeLayout, NodeLayout> shared = new LinkedHashMap<NodeLayout, NodeLayout>();
Iterator<NodeLayout> e = nodes.iterator();
while (e.hasNext()) {
NodeLayout nl = e.next();
if (nl.cofactor.equalsIgnoreCase("true")) {
continue;
}
NodeLayout nl2;
Iterator<NodeLayout> e2 = info2.nodes.iterator();
while (e2.hasNext()) {
nl2 = e2.next();
if (nl2.cofactor.equalsIgnoreCase("true")) {
continue;
}
if (nl.nodeID.equals(nl2.nodeID)) {
shared.put(nl, nl2);
}
}
}
return shared;
}
// ## operation generateSpeciesStatus(ReactionModel,ArrayList,ArrayList,ArrayList)
private LinkedHashMap generateSpeciesStatus(
ReactionModel p_reactionModel,
ArrayList p_speciesChemkinName,
ArrayList p_speciesConc,
ArrayList p_speciesFlux) {
// #[ operation generateSpeciesStatus(ReactionModel,ArrayList,ArrayList,ArrayList)
int size = p_speciesChemkinName.size();
if (size != p_speciesConc.size() || size != p_speciesFlux.size())
throw new InvalidSpeciesStatusException();
LinkedHashMap speStatus = new LinkedHashMap();
for (int i = 0; i < size; i++) {
String name = (String) p_speciesChemkinName.get(i);
int ID = parseIDFromChemkinName(name);
Species spe = SpeciesDictionary.getInstance().getSpeciesFromID(ID);
double conc = ((Double) p_speciesConc.get(i)).doubleValue();
double flux = ((Double) p_speciesFlux.get(i)).doubleValue();
System.out.println(
String.valueOf(spe.getID())
+ '\t'
+ spe.getName()
+ '\t'
+ String.valueOf(conc)
+ '\t'
+ String.valueOf(flux));
if (conc < 0) {
double aTol = ReactionModelGenerator.getAtol();
// if (Math.abs(conc) < aTol) conc = 0;
// else throw new NegativeConcentrationException("species " + spe.getName() + " has negative
// conc: " + String.valueOf(conc));
if (conc < -100.0 * aTol)
throw new NegativeConcentrationException(
"Species " + spe.getName() + " has negative concentration: " + String.valueOf(conc));
}
SpeciesStatus ss = new SpeciesStatus(spe, 1, conc, flux);
speStatus.put(spe, ss);
}
return speStatus;
// #]
}
// ## operation readReactorOutputFile(ReactionModel)
public SystemSnapshot readReactorOutputFile(ReactionModel p_reactionModel) {
// #[ operation readReactorOutputFile(ReactionModel)
try {
// open output file and build the DOM tree
String dir = System.getProperty("RMG.workingDirectory");
String filename = "chemkin/reactorOutput.xml";
File inputFile = new File(filename);
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setValidating(true); // validate the document with the DTD
factory.setIgnoringElementContentWhitespace(true); // ignore whitespace
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(inputFile);
// get root element and its children
Element root = doc.getDocumentElement();
NodeList rootchildren = root.getChildNodes();
// header is rootchildren.item(0)
// get return message and check for successful run
Element returnmessageElement = (Element) rootchildren.item(1);
Text returnmessageText = (Text) returnmessageElement.getFirstChild();
String returnmessage = returnmessageText.toString();
returnmessage = returnmessage.trim();
if (!returnmessage.contains("SUCCESSFULLY COMPLETED RUN.")) {
System.out.println("External reactor model failed!");
System.out.println("Reactor model error message: " + returnmessage);
System.exit(0);
}
// get outputvalues element and its children
Element outputvaluesElement = (Element) rootchildren.item(2);
NodeList children = outputvaluesElement.getChildNodes();
// get time
Element timeElement = (Element) children.item(0);
Text timeText = (Text) timeElement.getFirstChild();
double time = Double.parseDouble(timeText.getData());
String timeUnits = timeElement.getAttribute("units");
// get systemstate element and its children
Element systemstateElement = (Element) children.item(1);
NodeList states = systemstateElement.getChildNodes();
// get temperature and its units
Element temperatureElement = (Element) states.item(0);
String tempUnits = temperatureElement.getAttribute("units");
Text temperatureText = (Text) temperatureElement.getFirstChild();
double temp = Double.parseDouble(temperatureText.getData());
Temperature T = new Temperature(temp, tempUnits);
// get pressure and its units
Element pressureElement = (Element) states.item(1);
String presUnits = pressureElement.getAttribute("units");
Text pressureText = (Text) pressureElement.getFirstChild();
double pres = Double.parseDouble(pressureText.getData());
Pressure P = new Pressure(pres, presUnits);
// get species amounts (e.g. concentrations)
ArrayList speciesIDs = new ArrayList();
ArrayList amounts = new ArrayList();
ArrayList fluxes = new ArrayList();
String amountUnits = null;
String fluxUnits = null;
// loop thru all the species
// begin at i=2, since T and P take already the first two position of states
int nSpe = (states.getLength() - 2) / 2;
int index = 0;
LinkedHashMap inertGas = new LinkedHashMap();
for (int i = 2; i < nSpe + 2; i++) {
// get amount element and the units
Element amountElement = (Element) states.item(i);
amountUnits = amountElement.getAttribute("units");
Element fluxElement = (Element) states.item(i + nSpe);
fluxUnits = fluxElement.getAttribute("units");
// get speciesid and store in an array list
String thisSpeciesID = amountElement.getAttribute("speciesid");
// get amount (e.g. concentraion) and store in an array list
Text amountText = (Text) amountElement.getFirstChild();
double thisAmount = Double.parseDouble(amountText.getData());
if (thisAmount < 0) {
double aTol = ReactionModelGenerator.getAtol();
// if (Math.abs(thisAmount) < aTol) thisAmount = 0;
// else throw new NegativeConcentrationException("Negative concentration in
// reactorOutput.xml: " + thisSpeciesID);
if (thisAmount < -100.0 * aTol)
throw new NegativeConcentrationException(
"Species "
+ thisSpeciesID
+ " has negative concentration: "
+ String.valueOf(thisAmount));
}
// get amount (e.g. concentraion) and store in an array list
Text fluxText = (Text) fluxElement.getFirstChild();
double thisFlux = Double.parseDouble(fluxText.getData());
if (thisSpeciesID.compareToIgnoreCase("N2") == 0
|| thisSpeciesID.compareToIgnoreCase("Ne") == 0
|| thisSpeciesID.compareToIgnoreCase("Ar") == 0) {
inertGas.put(thisSpeciesID, new Double(thisAmount));
} else {
speciesIDs.add(index, thisSpeciesID);
amounts.add(index, new Double(thisAmount));
fluxes.add(index, new Double(thisFlux));
index++;
}
}
// print results for debugging purposes
/**
* System.out.println(returnmessage); System.out.println("Temp = " + temp + " " + tempUnits);
* System.out.println("Pres = " + pres + " " + presUnits); for (int i = 0; i < amounts.size();
* i++) { System.out.println(speciesIDs.get(i) + " " + amounts.get(i) + " " + amountUnits); }
*/
ReactionTime rt = new ReactionTime(time, timeUnits);
LinkedHashMap speStatus = generateSpeciesStatus(p_reactionModel, speciesIDs, amounts, fluxes);
SystemSnapshot ss = new SystemSnapshot(rt, speStatus, T, P);
ss.inertGas = inertGas;
return ss;
} catch (Exception e) {
System.out.println("Error reading reactor model output: " + e.getMessage());
System.exit(0);
return null;
}
// #]
}
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();
}
}
public boolean isEmpty() {
return nodes.isEmpty(); // && edges.isEmpty() && idToNode.isEmpty();
}
public void addEdgeLayout(
String sp, String s, String sc, String tp, String t, String tc, ArrayList<LayoutPoint> b) {
EdgeLayout el = new EdgeLayout(sp, s, sc, tp, t, tc);
el.setBends(b);
edges.add(el);
}
public void CrawlRT(String RTPage) throws IOException {
ArrayList<String> t = new ArrayList<String>();
String crawlData;
String crawlData2;
String crawlData3;
FileReader freader = new FileReader("Crawl.txt");
BufferedReader br = new BufferedReader(freader);
FileReader freader2 = new FileReader("Tocrawl.txt");
BufferedReader br2 = new BufferedReader(freader2);
FileWriter fwriter2 = new FileWriter("Tocrawl.txt", true);
BufferedWriter bw2 = new BufferedWriter(fwriter2);
FileWriter fwriter = new FileWriter("Crawl.txt", true);
BufferedWriter bw = new BufferedWriter(fwriter);
/*while(null != (crawlData2 = br.readLine()))
{
if(crawlData2 !=null)
Crawl.add(crawlData2);
}
t = collectLinks(RTPage);
Iterator<String> e3= t.iterator();
while(e3.hasNext())
{
String ee = e3.next();
if(!Crawl.contains(ee))
{
bw2.write(ee+"\r\n");
}
}
br.close();
br2.close();
bw.close();
bw2.close();*/
if (null == (crawlData = br.readLine()))
// if(true)
{
// initial iteration
bw.write(RTPage + "\r\n");
Crawl.add(RTPage);
t = collectLinks(RTPage);
ToCrawl.addAll(t);
} else {
// collect data from files and load to array lists
while (null != (crawlData2 = br.readLine())) {
if (crawlData2 != null) Crawl.add(crawlData2);
}
while (null != (crawlData3 = br2.readLine())) {
if (crawlData3 != null) ToCrawl.add(crawlData3);
}
}
System.out.println("Crawlled");
// Number of movies to be crawled
for (int i = 0; i < 1000; i++) {
if (ToCrawl.size() > 0) {
Crawl.removeAll(Collections.singleton(null));
ToCrawl.removeAll(Collections.singleton(null));
String c = ToCrawl.get(0);
if (Crawl.contains(c)) ToCrawl.remove(c);
else {
// collect links and collect data from a particular link
Crawl.add(c);
t = collectLinks(c);
CollectData(c);
ToCrawl.remove(c);
Iterator<String> e3 = t.iterator();
while (e3.hasNext()) {
String ee = e3.next();
if (!ToCrawl.contains(ee)) {
if (!Crawl.contains(ee)) {
ToCrawl.add(ee);
}
}
}
bw.write(c + "\r\n");
}
}
}
System.out.println("To Be Crawlled");
Iterator<String> e2 = ToCrawl.iterator();
while (e2.hasNext()) {
// write to file the movies still to be crawled.
bw2.write(e2.next() + "\r\n");
}
prop.setProperty("Id", Integer.toString(n));
prop.store(new FileOutputStream("config.properties"), null);
br.close();
br2.close();
bw.close();
bw2.close();
}
/**
* return a list of queues for connected groups of pathways place pathways according to the order
* of the queues and the list
*
* @param layouts
* @param dependOn the index number of pathway this one depends on, -1 if no dependency
* @return
*/
public static ArrayList<Queue> pathwayQueues(LayoutInfo[] layouts, int[] dependOn) {
ArrayList<Queue> queues =
new ArrayList<Queue>(); // each queue is for a disconnected group of pathways
int n = layouts.length;
boolean[] added = new boolean[n]; // whether the pathway is added into a queue
// boolean[] processed = new boolean[n];//whether all neighbours of this pathway are added into
// some queue
Queue<Integer> toProcess = new LinkedList<Integer>();
// current queue to add pathways into
// if not null, then exists a queue to add pathways into
// otherwise need to create a new queue(for disconnected group of pathways)
Queue currentQueue = null;
Arrays.sort(layouts, new LayoutBoxSizeComparator());
/*TODO delete
LayoutInfo tmp0 = layouts[0];
LayoutInfo tmp1 = layouts[1];
LayoutInfo tmp2 = layouts[2];
LayoutInfo tmp3 = layouts[3];
LayoutInfo tmp6 = layouts[6];
layouts[3]=tmp1;
layouts[2]=tmp6;
layouts[1]=tmp2;
layouts[6]=tmp0;
layouts[0] = tmp3;
/*
for(LayoutInfo i:layouts){
System.out.println(i.getExactLayoutBox().size());
}
//*/
for (int i = n - 1; i >= 0; i--) {
if (added[i]) {
continue;
}
currentQueue = new LinkedList<Integer>(); // current queue to add connected pathways into
queues.add(currentQueue);
toProcess.add(i);
currentQueue.add(i);
added[i] = true;
dependOn[i] = -1;
while (toProcess.size() != 0) {
int p = toProcess.remove();
for (int j = n - 2; j >= 0; j--) { // the first one is already added, so search from n-2
// find all non-visited neighbour pathways of layout[p]
if (added[j]) {
continue;
}
if (layouts[p].sharedNodes(layouts[j]).size() > 0 && !added[j]) {
currentQueue.add(j);
toProcess.add(j);
added[j] = true;
dependOn[j] = p;
}
}
// processed[p]=true;
}
currentQueue = null; // finished a connected group of pathways
}
return queues;
}
// empty this info object
public void clearInfo() {
nodes.clear();
edges.clear();
idToNode.clear();
}