/**
* Carries out preprocessing that makes JEuclid handle the document better.
*
* @param doc Document
*/
static void preprocessForJEuclid(Document doc) {
// underbrace and overbrace
NodeList list = doc.getElementsByTagName("mo");
for (int i = 0; i < list.getLength(); i++) {
Element mo = (Element) list.item(i);
String parentName = ((Element) mo.getParentNode()).getTagName();
if (parentName == null) {
continue;
}
if (parentName.equals("munder") && isTextChild(mo, "\ufe38")) {
mo.setAttribute("stretchy", "true");
mo.removeChild(mo.getFirstChild());
mo.appendChild(doc.createTextNode("\u23df"));
} else if (parentName.equals("mover") && isTextChild(mo, "\ufe37")) {
mo.setAttribute("stretchy", "true");
mo.removeChild(mo.getFirstChild());
mo.appendChild(doc.createTextNode("\u23de"));
}
}
// menclose for long division doesn't allow enough top padding. Oh, and
// <mpadded> isn't implemented. And there isn't enough padding to left of
// the bar either. Solve by adding an <mover> with just an <mspace> over#
// the longdiv, contained within an mrow that adds a <mspace> before it.
list = doc.getElementsByTagName("menclose");
for (int i = 0; i < list.getLength(); i++) {
Element menclose = (Element) list.item(i);
// Only for longdiv
if (!"longdiv".equals(menclose.getAttribute("notation"))) {
continue;
}
Element mrow = doc.createElementNS(WebMathsService.NS, "mrow");
Element mover = doc.createElementNS(WebMathsService.NS, "mover");
Element mspace = doc.createElementNS(WebMathsService.NS, "mspace");
Element mspaceW = doc.createElementNS(WebMathsService.NS, "mspace");
boolean previousElement = false;
for (Node previous = menclose.getPreviousSibling();
previous != null;
previous = previous.getPreviousSibling()) {
if (previous.getNodeType() == Node.ELEMENT_NODE) {
previousElement = true;
break;
}
}
if (previousElement) {
mspaceW.setAttribute("width", "4px");
}
menclose.getParentNode().insertBefore(mrow, menclose);
menclose.getParentNode().removeChild(menclose);
mrow.appendChild(mspaceW);
mrow.appendChild(mover);
mover.appendChild(menclose);
mover.appendChild(mspace);
}
}
private Element generatePortNode(Document doc, Port port) {
Element portEl = doc.createElement(EL_PORT);
portEl.setAttribute(ATR_NAME, port.getName());
portEl.setAttribute(ATR_TYPE, port.getType());
portEl.setAttribute(ATR_X, Integer.toString(port.getX()));
portEl.setAttribute(ATR_Y, Integer.toString(port.getY()));
portEl.setAttribute(ATR_PORT_CONNECTION, port.isArea() ? "area" : "");
portEl.setAttribute(ATR_STRICT, Boolean.toString(port.isStrict()));
portEl.setAttribute(ATR_MULTI, Boolean.toString(port.isMulti()));
return portEl;
}
private Node generateFieldNode(Document doc, ClassField field) {
Element fieldEl = doc.createElement(EL_FIELD);
fieldEl.setAttribute(ATR_NAME, field.getName());
fieldEl.setAttribute(ATR_TYPE, field.getType());
if (field.isInput()) fieldEl.setAttribute(ATR_NATURE, "input");
else if (field.isGoal()) fieldEl.setAttribute(ATR_NATURE, "goal");
if (field.getValue() != null) fieldEl.setAttribute(ATR_VALUE, field.getValue());
return fieldEl;
}
/**
* Creates an Element(or Node in XML in Document d) for single component
*
* @param x the component for which Element will be created
* @param d Where the element will be added
* @return the Element(for XML) created from component x
*/
private Element createCmpEle(component x, Document d) {
Element cmp_el = d.createElement("comp");
cmp_el.setAttribute("id", String.valueOf(x.getId()));
Element type_el = d.createElement("comp_type_id");
Text type_txt = d.createTextNode(String.valueOf(x.getType().getId()));
type_el.appendChild(type_txt);
cmp_el.appendChild(type_el);
Element pkg_el = d.createElement("pkg_name");
Text pkg_txt = d.createTextNode(x.getType().getType_pkg_name());
pkg_el.appendChild(pkg_txt);
cmp_el.appendChild(pkg_el);
Element pos_el = d.createElement("position");
Element x_el = d.createElement("x");
Text x_txt = d.createTextNode(String.valueOf(x.getPosition().x));
x_el.appendChild(x_txt);
pos_el.appendChild(x_el);
Element y_el = d.createElement("y");
Text y_txt = d.createTextNode(String.valueOf(x.getPosition().y));
y_el.appendChild(y_txt);
pos_el.appendChild(y_el);
cmp_el.appendChild(pos_el);
return cmp_el;
}
/**
* Creates an Element(or Node in XML in Document d) for single line
*
* @param x the line for which Element will be created
* @param d Where the element will be added
* @return the Element(for XML) created from line x
*/
private Element createWireEle(line x, Document d) {
Element wire_el = d.createElement("wire");
wire_el.setAttribute("id", String.valueOf(x.getId()));
Element strt_el = d.createElement("start");
Element strt_cmp_el = d.createElement("comp_id");
Text strt_cmp_txt = d.createTextNode(String.valueOf(x.getStartCmpId()));
strt_cmp_el.appendChild(strt_cmp_txt);
Element strt_mrk_el = d.createElement("mark_point");
Text strt_mrk_txt = d.createTextNode(String.valueOf(x.getStartMrkPt()));
strt_mrk_el.appendChild(strt_mrk_txt);
strt_el.appendChild(strt_cmp_el);
strt_el.appendChild(strt_mrk_el);
wire_el.appendChild(strt_el);
Element inter_el = d.createElement("inter_point");
inter_el.setAttribute("no", String.valueOf(x.getInter_Line_segs().size()));
for (Point p : x.getInter_Line_segs()) {
Element pos_el = d.createElement("position");
Element x_el = d.createElement("x");
Text x_txt = d.createTextNode(String.valueOf(p.x));
x_el.appendChild(x_txt);
pos_el.appendChild(x_el);
Element y_el = d.createElement("y");
Text y_txt = d.createTextNode(String.valueOf(p.y));
y_el.appendChild(y_txt);
pos_el.appendChild(y_el);
inter_el.appendChild(pos_el);
}
wire_el.appendChild(inter_el);
Element end_el = d.createElement("end");
Element end_cmp_el = d.createElement("comp_id");
Text end_cmp_txt = d.createTextNode(String.valueOf(x.getEndCmpId()));
end_cmp_el.appendChild(end_cmp_txt);
Element end_mrk_el = d.createElement("mark_point");
Text end_mrk_txt = d.createTextNode(String.valueOf(x.getEndMrkPt()));
end_mrk_el.appendChild(end_mrk_txt);
end_el.appendChild(end_cmp_el);
end_el.appendChild(end_mrk_el);
wire_el.appendChild(end_el);
return wire_el;
}
/**
* Save the XML description of the circuit
*
* @param output an output stream to write in
* @return true if the dump was successful, false either
*/
public boolean dumpToXml(OutputStream output) {
Document doc;
Element root;
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder;
try {
builder = factory.newDocumentBuilder();
doc = builder.newDocument();
} catch (ParserConfigurationException pce) {
System.err.println("dumpToXmlFile: unable to write XML save file.");
return false;
}
root = doc.createElement("Circuit");
root.setAttribute("name", this.getName());
for (iterNodes = this.nodes.iterator(); iterNodes.hasNext(); )
iterNodes.next().dumpToXml(doc, root);
root.normalize();
doc.appendChild(root);
try {
TransformerFactory tffactory = TransformerFactory.newInstance();
Transformer transformer = tffactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(output);
transformer.transform(source, result);
} catch (TransformerConfigurationException tce) {
System.err.println("dumpToXmlFile: Configuration Transformer exception.");
return false;
} catch (TransformerException te) {
System.err.println("dumpToXmlFile: Transformer exception.");
return false;
}
return true;
}
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();
}
}
@Override
public void produceVisibleOutput(QContent qc, boolean bInit, boolean bPlain) throws OmException {
// Get actual current value of string
String sCurrent = getQuestion().applyPlaceholders(sEquation);
if (bPlain) {
// Put text equivalent
Element eDiv =
qc.createElement("div"); // Can't use span because they aren't allowed to contain things
eDiv.setAttribute("style", "display:inline");
qc.addInlineXHTML(eDiv);
XML.createText(eDiv, (bSpaceBefore ? " " : "") + getString("alt") + (bSpaceAfter ? " " : ""));
qc.addTextEquivalent(getString("alt"));
// Put each placeholder
for (int i = 0; i < apPlaces.length; i++) {
// Check content is not hidden
Place p = apPlaces[i];
if ((!p.bImplicit && !p.qc.isDisplayed()) || (p.bImplicit && !p.qc.isChildDisplayed()))
continue;
// Label followed by content of placeholder
Element ePlace = XML.createChild(eDiv, "div");
if (p.sLabel != null) {
Element eLabel = XML.createChild(ePlace, p.sLabelFor == null ? "span" : "label");
XML.createText(eLabel, p.sLabel + " ");
qc.addTextEquivalent(p.sLabel);
if (p.sLabelFor != null)
eLabel.setAttribute(
"for", LabelComponent.getLabel(getQDocument(), bPlain, p.sLabelFor));
}
qc.setParent(ePlace);
p.qc.produceOutput(qc, bInit, bPlain);
qc.unsetParent();
}
} else {
// Check background colour, foreground, and zoom
Color cBackground = getBackground();
if (cBackground == null) cBackground = Color.white;
Color cForeground =
getQuestion().isFixedColour()
? convertRGB(getQuestion().getFixedColourFG())
: Color.black;
double dZoom = getQuestion().getZoom();
// Hash to filename/identifier
String sFilename =
"eq"
+ (sCurrent.hashCode()
+ cBackground.hashCode() * 3
+ cForeground.hashCode() * 7
+ (new Double(dZoom)).hashCode() * 11)
+ (getBoolean(PROPERTY_TEXTFONT) ? "t" : "e")
+ ".png";
// Make actual image if needed, also get placeholder positions
if (!sFilename.equals(sSent)) {
e = Equation.create(sCurrent, (float) dZoom);
if (getBoolean(PROPERTY_TEXTFONT)) e.setFont("Verdana", new int[] {13, 11, 9});
BufferedImage bi = e.render(cForeground, cBackground, true);
qc.addResource(sFilename, "image/png", QContent.convertPNG(bi));
for (int i = 0; i < apPlaces.length; i++) {
Point p = e.getPlaceholder(apPlaces[i].sID);
apPlaces[i].iActualX = p.x;
apPlaces[i].iActualY = p.y;
}
sSent = sFilename;
}
Element eEnsureSpaces = qc.createElement("div");
eEnsureSpaces.setAttribute("class", "equation");
qc.addInlineXHTML(eEnsureSpaces);
// If there's a space before, add one here too (otherwise IE eats it)
if (bSpaceBefore) XML.createText(eEnsureSpaces, " ");
String sImageID = QDocument.ID_PREFIX + getID() + "_img";
Element eImg = XML.createChild(eEnsureSpaces, "img");
eImg.setAttribute("id", sImageID);
eImg.setAttribute("onmousedown", "return false;"); // Prevent Firefox drag/drop
eImg.setAttribute("src", "%%RESOURCES%%/" + sFilename);
eImg.setAttribute("alt", getString("alt"));
eImg.setAttribute("style", "vertical-align:-" + (e.getHeight() - e.getBaseline()) + "px;");
if (bSpaceAfter) XML.createText(eEnsureSpaces, " ");
qc.addTextEquivalent(getString("alt"));
String sJavascript = "addOnLoad(function() { inlinePositionFix('" + sImageID + "'";
for (int i = 0; i < apPlaces.length; i++) {
Place p = apPlaces[i];
// Must get the label even though not using it, just to indicate that
// it's been used
if (p.sLabelFor != null) LabelComponent.getLabel(getQDocument(), bPlain, p.sLabelFor);
int iEffectiveWidth = (int) Math.round(dZoom * p.iWidth),
iEffectiveHeight = (int) Math.round(dZoom * p.iHeight);
String sPlaceholderID = QDocument.ID_PREFIX + getID() + "_" + p.sID;
Element ePlace = XML.createChild(eEnsureSpaces, "div");
ePlace.setAttribute("class", "placeholder");
ePlace.setAttribute("id", sPlaceholderID);
ePlace.setAttribute(
"style",
"width:"
+ iEffectiveWidth
+ "px; "
+ "height:"
+ iEffectiveHeight
+ "px; "
+ "visibility:hidden;");
QComponent qcPlaceComponent = p.qc;
if (qcPlaceComponent.isPropertyDefined(PROPERTY_FORCEWIDTH)
&& qcPlaceComponent.isPropertyDefined(PROPERTY_FORCEHEIGHT)) {
qcPlaceComponent.setInteger(PROPERTY_FORCEWIDTH, iEffectiveWidth);
qcPlaceComponent.setInteger(PROPERTY_FORCEHEIGHT, iEffectiveHeight);
}
if (p.sLabel != null) qc.addTextEquivalent(p.sLabel);
qc.setParent(ePlace);
qcPlaceComponent.produceOutput(qc, bInit, bPlain);
qc.unsetParent();
sJavascript += ",['" + sPlaceholderID + "'," + p.iActualX + "," + p.iActualY + "]";
}
sJavascript += "); });";
if (apPlaces.length > 0) // No JS needed if there weren't any placeholders
{
Element eScript = XML.createChild(eEnsureSpaces, "script");
eScript.setAttribute("type", "text/javascript");
XML.createText(eScript, sJavascript);
}
}
}
private Element generateGraphicsNode(Document doc, ClassGraphics gr) {
Element graphicsEl = doc.createElement(EL_GRAPHICS);
Element bounds = doc.createElement(EL_BOUNDS);
graphicsEl.appendChild(bounds);
bounds.setAttribute(ATR_X, Integer.toString(gr.getBoundX()));
bounds.setAttribute(ATR_Y, Integer.toString(gr.getBoundY()));
bounds.setAttribute(ATR_WIDTH, Integer.toString(gr.getBoundWidth()));
bounds.setAttribute(ATR_HEIGHT, Integer.toString(gr.getBoundHeight()));
for (Shape shape : gr.getShapes()) {
if (shape instanceof Rect) {
Rect rect = (Rect) shape;
Element rectEl = doc.createElement(EL_RECT);
graphicsEl.appendChild(rectEl);
rectEl.setAttribute(ATR_X, Integer.toString(rect.getX()));
rectEl.setAttribute(ATR_Y, Integer.toString(rect.getY()));
rectEl.setAttribute(ATR_WIDTH, Integer.toString(rect.getWidth()));
rectEl.setAttribute(ATR_HEIGHT, Integer.toString(rect.getHeight()));
rectEl.setAttribute(ATR_COLOUR, Integer.toString(rect.getColor().getRGB()));
rectEl.setAttribute(ATR_FILLED, Boolean.toString(rect.isFilled()));
rectEl.setAttribute(ATR_FIXED, Boolean.toString(rect.isFixed()));
rectEl.setAttribute(ATR_STROKE, Float.toString(rect.getStroke().getLineWidth()));
rectEl.setAttribute(ATR_LINETYPE, Float.toString(rect.getLineType()));
rectEl.setAttribute(ATR_TRANSPARENCY, Integer.toString(rect.getTransparency()));
} else if (shape instanceof Text) {
Text text = (Text) shape;
Element textEl = doc.createElement(EL_TEXT);
textEl.setAttribute(ATR_STRING, text.getText());
textEl.setAttribute(ATR_X, Integer.toString(text.getX()));
textEl.setAttribute(ATR_Y, Integer.toString(text.getY()));
textEl.setAttribute(ATR_FONTNAME, text.getFont().getName());
textEl.setAttribute(ATR_FONTSIZE, Integer.toString(text.getFont().getSize()));
textEl.setAttribute(ATR_FONTSTYLE, Integer.toString(text.getFont().getStyle()));
textEl.setAttribute(ATR_TRANSPARENCY, Integer.toString(text.getTransparency()));
textEl.setAttribute(ATR_COLOUR, Integer.toString(text.getColor().getRGB()));
graphicsEl.appendChild(textEl);
} // TODO handle the rest of shapes
}
return graphicsEl;
}
public void addPackageClass(PackageClass pClass) {
Document doc;
try {
doc = getDocument();
} catch (Exception e) {
e.printStackTrace();
return;
}
String name = pClass.getName();
// check if such class exists and remove duplicates
Element rootEl = doc.getDocumentElement();
NodeList classEls = rootEl.getElementsByTagName(EL_CLASS);
for (int i = 0; i < classEls.getLength(); i++) {
Element nameEl = getElementByName((Element) classEls.item(i), EL_NAME);
if (name.equals(nameEl.getTextContent())) {
rootEl.removeChild(classEls.item(i));
}
}
Element classNode = doc.createElement(EL_CLASS);
doc.getDocumentElement().appendChild(classNode);
classNode.setAttribute(ATR_TYPE, PackageClass.ComponentType.SCHEME.getXmlName());
classNode.setAttribute(ATR_STATIC, "false");
Element className = doc.createElement(EL_NAME);
className.setTextContent(name);
classNode.appendChild(className);
Element desrc = doc.createElement(EL_DESCRIPTION);
desrc.setTextContent(pClass.getDescription());
classNode.appendChild(desrc);
Element icon = doc.createElement(EL_ICON);
icon.setTextContent(pClass.getIcon());
classNode.appendChild(icon);
// graphics
classNode.appendChild(generateGraphicsNode(doc, pClass.getGraphics()));
// ports
List<Port> ports = pClass.getPorts();
if (!ports.isEmpty()) {
Element portsEl = doc.createElement(EL_PORTS);
classNode.appendChild(portsEl);
for (Port port : ports) {
portsEl.appendChild(generatePortNode(doc, port));
}
}
// fields
Collection<ClassField> fields = pClass.getFields();
if (!fields.isEmpty()) {
Element fieldsEl = doc.createElement(EL_FIELDS);
classNode.appendChild(fieldsEl);
for (ClassField cf : fields) {
fieldsEl.appendChild(generateFieldNode(doc, cf));
}
}
// write
try {
writeDocument(doc, new FileOutputStream(xmlFile));
} catch (FileNotFoundException e) {
e.printStackTrace();
}
}
