/**
* Serialize an object to a byte array. (code by CB)
*
* @param object object to serialize
* @return byte array that represents the object
* @throws Exception
*/
public static byte[] toByte(Object object) throws Exception {
ByteArrayOutputStream os = new ByteArrayOutputStream();
ObjectOutputStream oos = new ObjectOutputStream((OutputStream) os);
oos.writeObject(object);
oos.close();
return os.toByteArray();
}
public static String zip(String param) {
try {
byte[] unzip = param.getBytes("UTF-8");
ByteArrayInputStream bif = new ByteArrayInputStream(unzip);
ByteArrayOutputStream zipbof = new ByteArrayOutputStream();
// DeflaterOutputStream dos = new DeflaterOutputStream(zipbof);
GZIPOutputStream gos = new GZIPOutputStream(zipbof);
int position = 0;
for (int read_byte = 0; (read_byte = bif.read()) != -1; position++) {
// dos.write(read_byte);
gos.write(read_byte);
}
// dos.finish();
gos.finish();
zipbof.flush();
byte[] zipbyteArray = zipbof.toByteArray();
// return new sun.misc.BASE64Encoder().encode(zipbyteArray);
return Base64.encodeBase64String(zipbyteArray);
} catch (Exception ex) {
return null;
}
}
/** Reads the chunk of data to be imported from the request's input stream. */
private byte[] readChunk(HttpServletRequest req, int chunkSize) throws IOException {
ServletInputStream requestStream = req.getInputStream();
String contentType = req.getHeader(ProtocolConstants.HEADER_CONTENT_TYPE);
if (contentType.startsWith("multipart")) // $NON-NLS-1$
return readMultiPartChunk(requestStream, contentType);
ByteArrayOutputStream outputStream = new ByteArrayOutputStream(chunkSize);
IOUtilities.pipe(requestStream, outputStream, false, false);
return outputStream.toByteArray();
}
private Class<?> getClassFromStream(
final InputStream stream, final String classname, final File container)
throws IOException, SecurityException {
final ByteArrayOutputStream baos = new ByteArrayOutputStream();
int bytesRead = -1;
final byte[] buffer = new byte[8192];
while ((bytesRead = stream.read(buffer, 0, 8192)) != -1) {
baos.write(buffer, 0, bytesRead);
}
final byte[] classData = baos.toByteArray();
return this.defineClassFromData(container, classData, classname);
}
@Override
public byte[] getFollowRequests(UserPublicKey owner) {
byte[] dummy = null;
FollowRequestData request = new FollowRequestData(owner, dummy);
RowData[] requests = request.select();
if (requests == null) return new byte[4];
ByteArrayOutputStream bout = new ByteArrayOutputStream();
DataOutput dout = new DataOutputStream(bout);
try {
dout.writeInt(requests.length);
for (RowData req : requests) Serialize.serialize(req.data, dout);
return bout.toByteArray();
} catch (IOException e) {
e.printStackTrace();
return null;
}
}
public static void main(String[] args) {
try {
SerializableZipFile szf = new SerializableZipFile(args[0]);
ByteArrayOutputStream bout = new ByteArrayOutputStream();
ObjectOutputStream oout = new ObjectOutputStream(bout);
oout.writeObject(szf);
oout.close();
System.out.println("Wrote object!");
ByteArrayInputStream bin = new ByteArrayInputStream(bout.toByteArray());
ObjectInputStream oin = new ObjectInputStream(bin);
Object o = oin.readObject();
System.out.println("Read object!");
} catch (Exception ex) {
ex.printStackTrace();
}
}
private byte[] readBytes(InputStream in) {
byte[] result = null;
try {
ByteArrayOutputStream out = new ByteArrayOutputStream();
byte[] buffer = new byte[BUFFER_SIZE];
int bytesRead = 0;
while ((bytesRead = in.read(buffer, 0, BUFFER_SIZE)) != -1) {
out.write(buffer, 0, bytesRead);
}
out.close();
result = out.toByteArray();
} catch (IOException ex) {
Logger.getLogger(getClass()).debug("Error loading Zip entry", ex);
}
return (result);
}
/**
* Zips byte array.
*
* @param input Input bytes.
* @param initBufSize Initial buffer size.
* @return Zipped byte array.
* @throws IOException If failed.
*/
public static byte[] zipBytes(byte[] input, int initBufSize) throws IOException {
ByteArrayOutputStream bos = new ByteArrayOutputStream(initBufSize);
try (ZipOutputStream zos = new ZipOutputStream(bos)) {
ZipEntry entry = new ZipEntry("");
try {
entry.setSize(input.length);
zos.putNextEntry(entry);
zos.write(input);
} finally {
zos.closeEntry();
}
}
return bos.toByteArray();
}
@Override
public byte[] getAllUsernamesGzip() throws IOException {
try (PreparedStatement stmt = conn.prepareStatement("select name from users")) {
ResultSet rs = stmt.executeQuery();
List<String> list = new ArrayList<>();
while (rs.next()) {
String username = rs.getString("name");
list.add(username);
}
ByteArrayOutputStream bout = new ByteArrayOutputStream();
try (DataOutputStream dout = new DataOutputStream(new GZIPOutputStream(bout))) {
for (String uname : list) Serialize.serialize(uname, dout);
}
return bout.toByteArray();
} catch (SQLException sqe) {
throw new IOException(sqe);
}
}
// Takes a PImage and compresses it into a JPEG byte stream
// Adapted from Dan Shiffman's UDP Sender code
public byte[] compressImage(PImage img) {
// We need a buffered image to do the JPG encoding
BufferedImage bimg = new BufferedImage(img.width, img.height, BufferedImage.TYPE_INT_RGB);
img.loadPixels();
bimg.setRGB(0, 0, img.width, img.height, img.pixels, 0, img.width);
// Need these output streams to get image as bytes for UDP communication
ByteArrayOutputStream baStream = new ByteArrayOutputStream();
BufferedOutputStream bos = new BufferedOutputStream(baStream);
// Turn the BufferedImage into a JPG and put it in the BufferedOutputStream
// Requires try/catch
try {
ImageIO.write(bimg, "jpg", bos);
} catch (IOException e) {
e.printStackTrace();
}
// Get the byte array, which we will send out via UDP!
return baStream.toByteArray();
}
public static String unzip(String param) {
try {
// byte[] zipArray = new sun.misc.BASE64Decoder().decodeBuffer(param);
byte[] zipArray = Base64.decodeBase64(param);
ByteArrayInputStream bif = new ByteArrayInputStream(zipArray);
// InflaterInputStream iis = new InflaterInputStream(bif);
GZIPInputStream gis = new GZIPInputStream(bif);
ByteArrayOutputStream unZipbof = new ByteArrayOutputStream();
int position = 0;
// for (int read_byte = 0; (read_byte = iis.read()) != -1; position++) {
for (int read_byte = 0; (read_byte = gis.read()) != -1; position++) {
unZipbof.write(read_byte);
}
unZipbof.flush();
byte[] unZipbyteArray = unZipbof.toByteArray();
String returnUnZipString = new String(unZipbyteArray, "UTF-8");
return returnUnZipString;
} catch (Exception ex) {
return null;
}
}
public Hashtable processData(
ServletInputStream is, String boundary, String saveInDir, int clength)
throws IllegalArgumentException, IOException {
if (is == null) throw new IllegalArgumentException("InputStream");
if (boundary == null || boundary.trim().length() < 1)
throw new IllegalArgumentException("\"" + boundary + "\" is an illegal boundary indicator");
boundary = "--" + boundary;
StringTokenizer stLine = null, stFields = null;
FileInfo fileInfo = null;
Hashtable dataTable = new Hashtable(5);
String line = null, field = null, paramName = null;
boolean saveFiles = (saveInDir != null && saveInDir.trim().length() > 0);
boolean isFile = false;
if (saveFiles) { // Create the required directory (including parent dirs)
File f = new File(saveInDir);
f.mkdirs();
}
line = getLine(is);
if (line == null || !line.startsWith(boundary))
throw new IOException("Boundary not found; boundary = " + boundary + ", line = " + line);
while (line != null) {
if (line == null || !line.startsWith(boundary)) return dataTable;
line = getLine(is);
if (line == null) return dataTable;
stLine = new StringTokenizer(line, ";\r\n");
if (stLine.countTokens() < 2) throw new IllegalArgumentException("Bad data in second line");
line = stLine.nextToken().toLowerCase();
if (line.indexOf("form-data") < 0)
throw new IllegalArgumentException("Bad data in second line");
stFields = new StringTokenizer(stLine.nextToken(), "=\"");
if (stFields.countTokens() < 2)
throw new IllegalArgumentException("Bad data in second line");
fileInfo = new FileInfo();
stFields.nextToken();
paramName = stFields.nextToken();
isFile = false;
if (stLine.hasMoreTokens()) {
field = stLine.nextToken();
stFields = new StringTokenizer(field, "=\"");
if (stFields.countTokens() > 1) {
if (stFields.nextToken().trim().equalsIgnoreCase("filename")) {
fileInfo.name = paramName;
String value = stFields.nextToken();
if (value != null && value.trim().length() > 0) {
fileInfo.clientFileName = value;
isFile = true;
} else {
line = getLine(is); // Skip "Content-Type:" line
line = getLine(is); // Skip blank line
line = getLine(is); // Skip blank line
line = getLine(is); // Position to boundary line
continue;
}
}
} else if (field.toLowerCase().indexOf("filename") >= 0) {
line = getLine(is); // Skip "Content-Type:" line
line = getLine(is); // Skip blank line
line = getLine(is); // Skip blank line
line = getLine(is); // Position to boundary line
continue;
}
}
boolean skipBlankLine = true;
if (isFile) {
line = getLine(is);
if (line == null) return dataTable;
if (line.trim().length() < 1) skipBlankLine = false;
else {
stLine = new StringTokenizer(line, ": ");
if (stLine.countTokens() < 2)
throw new IllegalArgumentException("Bad data in third line");
stLine.nextToken(); // Content-Type
fileInfo.fileContentType = stLine.nextToken();
}
}
if (skipBlankLine) {
line = getLine(is);
if (line == null) return dataTable;
}
if (!isFile) {
line = getLine(is);
if (line == null) return dataTable;
dataTable.put(paramName, line);
// If parameter is dir, change saveInDir to dir
if (paramName.equals("dir")) saveInDir = line;
line = getLine(is);
continue;
}
try {
UplInfo uplInfo = new UplInfo(clength);
UploadMonitor.set(fileInfo.clientFileName, uplInfo);
OutputStream os = null;
String path = null;
if (saveFiles)
os = new FileOutputStream(path = getFileName(saveInDir, fileInfo.clientFileName));
else os = new ByteArrayOutputStream(ONE_MB);
boolean readingContent = true;
byte previousLine[] = new byte[2 * ONE_MB];
byte temp[] = null;
byte currentLine[] = new byte[2 * ONE_MB];
int read, read3;
if ((read = is.readLine(previousLine, 0, previousLine.length)) == -1) {
line = null;
break;
}
while (readingContent) {
if ((read3 = is.readLine(currentLine, 0, currentLine.length)) == -1) {
line = null;
uplInfo.aborted = true;
break;
}
if (compareBoundary(boundary, currentLine)) {
os.write(previousLine, 0, read - 2);
line = new String(currentLine, 0, read3);
break;
} else {
os.write(previousLine, 0, read);
uplInfo.currSize += read;
temp = currentLine;
currentLine = previousLine;
previousLine = temp;
read = read3;
} // end else
} // end while
os.flush();
os.close();
if (!saveFiles) {
ByteArrayOutputStream baos = (ByteArrayOutputStream) os;
fileInfo.setFileContents(baos.toByteArray());
} else fileInfo.file = new File(path);
dataTable.put(paramName, fileInfo);
uplInfo.currSize = uplInfo.totalSize;
} // end try
catch (IOException e) {
throw e;
}
}
return dataTable;
}
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 byte[] ZipIt(ArrayList<ResultType> items, String[] algorithm, String[] filetype)
throws IOException {
ByteArrayOutputStream baos = new ByteArrayOutputStream();
ZipOutputStream zos = new ZipOutputStream(baos);
BufferedInputStream bis;
String[] files = new String[10000];
File file;
int bytesRead;
byte[] buffer = new byte[1024];
int j = 0;
boolean flag;
for (int i = 0; i < items.size(); i++) {
ResultType g = (ResultType) items.get(i);
String folder = g.get("genomeNames");
file = new File("/storage/brcdownloads/patric2/genomes/" + folder);
if (!file.exists()) {
System.err.println("Skipping Folder: " + "/storage/brcdownloads/patric2/genomes/" + folder);
continue;
} else {
for (int k = 0; k < algorithm.length; k++) {
for (int m = 0; m < filetype.length; m++) {
flag = false;
file =
new File(
"/storage/brcdownloads/patric2/genomes/"
+ folder
+ "/"
+ folder
+ (filetype[m].equals(".fna") ? "" : algorithm[k])
+ filetype[m]);
if (!file.exists()) {
System.err.println("Skipping File: " + file.getAbsolutePath());
} else {
// System.out.println("File: " + file.getAbsolutePath());
for (int z = 0; z < files.length; z++) {
if (files[z] != null && files[z].equals(file.getAbsolutePath())) {
flag = true;
break;
}
}
// System.out.println(flag);
if (!flag) {
files[j] = file.getAbsolutePath();
j++;
}
}
}
}
}
}
// System.out.println(j);
if (j > 0) {
for (int i = 0; i < j; i++) {
file = new File(files[i]);
bis = new BufferedInputStream(new FileInputStream(file));
ZipEntry entry = new ZipEntry(file.getName());
zos.putNextEntry(entry);
while ((bytesRead = bis.read(buffer)) != -1) {
zos.write(buffer, 0, bytesRead);
}
bis.close();
zos.closeEntry();
}
zos.close();
}
return baos.toByteArray();
}