public static BufferedImage convertImageData(ImageData data) {
BufferedImage bimg = null;
int height = data.getHeight(), width = data.getWidth();
Object pixels = data.getData();
if (pixels instanceof int[] && data.getElementWidth() == 1) {
int[] arr = (int[]) pixels;
byte[] barray = new byte[arr.length * 3];
int k = 0;
for (int j = 0; j < arr.length; j++) {
int l = arr[j];
barray[k++] = (byte) (l & 0xFF);
barray[k++] = (byte) ((l >>> 8) & 0xFF);
barray[k++] = (byte) ((l >>> 16) & 0xFF);
}
ColorModel ccm =
new ComponentColorModel(
ICC_ColorSpace.getInstance(ICC_ColorSpace.CS_sRGB),
new int[] {8, 8, 8},
false,
false,
Transparency.OPAQUE,
DataBuffer.TYPE_BYTE);
DataBuffer bbuf = new DataBufferByte(barray, barray.length);
SampleModel bmodel =
new PixelInterleavedSampleModel(
DataBuffer.TYPE_BYTE, width, height, 3, 3 * width, new int[] {2, 1, 0});
WritableRaster raster = Raster.createWritableRaster(bmodel, bbuf, new Point(0, 0));
bimg = new BufferedImage(ccm, raster, false, new Hashtable());
} else if (pixels instanceof byte[]
&& data.getElementWidth() == 1) { // Assume gray scale model?
byte[] arr = (byte[]) pixels;
byte[] barray = new byte[arr.length * 3];
int k = 0;
for (int j = 0; j < arr.length; j++) {
byte l = arr[j];
barray[k++] = l;
barray[k++] = l;
barray[k++] = l;
}
ColorModel ccm =
new ComponentColorModel(
ICC_ColorSpace.getInstance(ICC_ColorSpace.CS_sRGB),
new int[] {8, 8, 8},
false,
false,
Transparency.OPAQUE,
DataBuffer.TYPE_BYTE);
DataBuffer bbuf = new DataBufferByte(barray, barray.length);
SampleModel bmodel =
new PixelInterleavedSampleModel(
DataBuffer.TYPE_BYTE, width, height, 3, 3 * width, new int[] {2, 1, 0});
WritableRaster raster = Raster.createWritableRaster(bmodel, bbuf, new Point(0, 0));
bimg = new BufferedImage(ccm, raster, false, new Hashtable());
} else {
throw new RuntimeException("Unexpected data.");
}
return bimg;
}
// returns a value specifying some kind of average brightness in the image.
protected int getAverageBrightness(BufferedImage img) {
Raster r = img.getData();
int total = 0;
for (int y = 0; y < r.getHeight(); y++) {
for (int x = 0; x < r.getWidth(); x++) {
total += r.getSample(r.getMinX() + x, r.getMinY() + y, 0);
}
}
return (int) (total / ((r.getWidth() / factorD) * (r.getHeight() / factorD)));
}
public void decode() throws IOException {
readTagDescriptors();
final MessageDigest md;
try {
md = MessageDigest.getInstance("SHA-512");
} catch (NoSuchAlgorithmException e) {
e.printStackTrace();
return;
}
final ComponentColorModel colorModel =
new ComponentColorModel(
ColorSpace.getInstance(ColorSpace.CS_sRGB),
true,
false,
Transparency.TRANSLUCENT,
DataBuffer.TYPE_BYTE);
final int[] bandOffsets = {2, 1, 0, 3};
final Map<String, String> duplicateGuard = new HashMap<String, String>();
final byte[] bytes = data.array();
final int[] tags = new int[8];
final List<String> symLinkCommand = new ArrayList<String>(4);
symLinkCommand.add("ln");
symLinkCommand.add("-s");
symLinkCommand.add(null);
symLinkCommand.add(null);
for (int fileIndex = 0; fileIndex < fileCount; fileIndex++) {
data.position(fileDescriptorsOffset + ((4 + 8) * fileIndex));
final int fileDataOffset = data.getInt();
int numOfTags = 8;
for (int i = 0; i < 8; i++) {
int tag = data.get() & 0xff;
if (tag == 0) {
numOfTags = i;
break;
}
tags[i] = tag;
}
data.position(fileDataSectionOffset + fileDataOffset);
final int artRows = data.getShort();
final int artColumns = data.getShort();
// skip unknown
data.position(data.position() + 28);
final int[] subimageOffsets = readNumericArray(9, false);
final int[] subimageWidths = readNumericArray(9, true);
final int[] subimageHeights = readNumericArray(9, true);
assert numOfTags >= 2;
final File dir;
final int tagStartIndexForFilename;
if (numOfTags == 2) {
tagStartIndexForFilename = 1;
dir = new File(outputDir, names[tags[0]].toString());
} else {
tagStartIndexForFilename = 2;
dir = new File(outputDir, names[tags[0]] + "/" + names[tags[1]]);
}
boolean dirCreated = false;
final int imageCount = artRows * artColumns;
for (int subImageIndex = 0; subImageIndex < imageCount; subImageIndex++) {
final int w = subimageWidths[subImageIndex];
final int h = subimageHeights[subImageIndex];
if (w <= 0 || h <= 0) {
continue;
}
final int srcPos = fileDataSectionOffset + fileDataOffset + subimageOffsets[subImageIndex];
final int srcLength = w * h * 4;
md.update(bytes, srcPos, srcLength);
md.update((byte) w);
md.update((byte) h);
final String digest = convertToHex(md.digest());
md.reset();
if (!dirCreated) {
//noinspection ResultOfMethodCallIgnored
dir.mkdirs();
dirCreated = true;
}
final byte[] bgra = new byte[srcLength];
// cannot pass bytes directly, offset in DataBufferByte is not working
System.arraycopy(bytes, srcPos, bgra, 0, bgra.length);
BufferedImage image =
new BufferedImage(
colorModel,
(WritableRaster)
Raster.createRaster(
new PixelInterleavedSampleModel(
DataBuffer.TYPE_BYTE, w, h, 4, w * 4, bandOffsets),
new DataBufferByte(bgra, bgra.length),
null),
false,
null);
final StringBuilder outFilename =
createOutpuFile(
numOfTags, tags, tagStartIndexForFilename, imageCount > 0, subImageIndex);
final String oldOutFilename = duplicateGuard.get(digest);
if (oldOutFilename == null) {
File file = new File(dir, outFilename.toString());
duplicateGuard.put(digest, file.getPath());
ImageIO.write(image, "png", file);
} else {
symLinkCommand.set(2, oldOutFilename);
symLinkCommand.set(3, dir + "/" + outFilename);
Process process = new ProcessBuilder(symLinkCommand).start();
try {
if (process.waitFor() != 0) {
throw new IOException(
"Can't create symlink " + symLinkCommand.get(2) + " " + symLinkCommand.get(3));
}
} catch (InterruptedException e) {
throw new IOException(e);
}
}
}
}
}
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();
}
}
/** Convert standard img to a buffered image. */
public static BufferedImage convertImage(Image img) {
int height = img.getHeight(null), width = img.getWidth(null);
// FloatMatrix fm = new FloatMatrix( height, width ) ;
PixelGrabber grabber = new PixelGrabber(img, 0, 0, width, height, false);
try {
grabber.grabPixels();
} catch (InterruptedException e) {
System.out.println(e);
}
Object pixels = grabber.getPixels();
ColorModel cm = grabber.getColorModel();
BufferedImage bimg = null;
// REVISIT Makes some unwarranted assumptions about the layout of the PixelGrabber data
// as being either int (ARGB?) or byte (gray scale?)
if (pixels instanceof int[]) {
int[] arr = (int[]) pixels;
byte[] barray = new byte[arr.length * 3];
int k = 0;
for (int j = 0; j < arr.length; j++) {
int l = arr[j];
barray[k++] = (byte) (l & 0xFF);
barray[k++] = (byte) ((l >>> 8) & 0xFF);
barray[k++] = (byte) ((l >>> 16) & 0xFF);
}
ColorModel ccm =
new ComponentColorModel(
ICC_ColorSpace.getInstance(ICC_ColorSpace.CS_sRGB),
new int[] {8, 8, 8},
false,
false,
Transparency.OPAQUE,
DataBuffer.TYPE_BYTE);
DataBuffer bbuf = new DataBufferByte(barray, barray.length);
SampleModel bmodel =
new PixelInterleavedSampleModel(
DataBuffer.TYPE_BYTE, width, height, 3, 3 * width, new int[] {2, 1, 0});
WritableRaster raster = Raster.createWritableRaster(bmodel, bbuf, new Point(0, 0));
bimg = new BufferedImage(ccm, raster, false, new Hashtable());
} else if (pixels instanceof byte[]) { // Assume gray scale model?
byte[] arr = (byte[]) pixels;
byte[] barray = new byte[arr.length * 3];
int k = 0;
for (int j = 0; j < arr.length; j++) {
byte l = arr[j];
barray[k++] = l;
barray[k++] = l;
barray[k++] = l;
}
ColorModel ccm =
new ComponentColorModel(
ICC_ColorSpace.getInstance(ICC_ColorSpace.CS_sRGB),
new int[] {8, 8, 8},
false,
false,
Transparency.OPAQUE,
DataBuffer.TYPE_BYTE);
DataBuffer bbuf = new DataBufferByte(barray, barray.length);
SampleModel bmodel =
new PixelInterleavedSampleModel(
DataBuffer.TYPE_BYTE, width, height, 3, 3 * width, new int[] {2, 1, 0});
WritableRaster raster = Raster.createWritableRaster(bmodel, bbuf, new Point(0, 0));
bimg = new BufferedImage(ccm, raster, false, new Hashtable());
} else {
throw new RuntimeException("Unexpected data.");
}
return bimg;
}
/**
* Loads PNG files and returns the result as an int[][]. The only PNG formats permitted are those
* with up to 256 grays (including simple black and white) or indexed colors from an up to
* 256-sized color table. Each integer value represents the gray level or the color table index
* value of the pixel. The Y dimension is not flipped.
*/
public static int[][] loadPNGFile(InputStream str) throws IOException {
// read the bytes into a byte array
BufferedInputStream stream = new BufferedInputStream(str);
ArrayList list = new ArrayList();
int count = 0;
while (true) {
byte[] buffer = new byte[16384 * 16];
int len = stream.read(buffer);
if (len <= 0) // all done
break;
else if (len < buffer.length) {
byte[] buf2 = new byte[len];
System.arraycopy(buffer, 0, buf2, 0, len);
buffer = buf2;
}
count += len;
list.add(buffer);
}
byte[] data = new byte[count];
int cur = 0;
for (int i = 0; i < list.size(); i++) {
byte[] b = (byte[]) (list.get(i));
System.arraycopy(b, 0, data, cur, b.length);
cur += b.length;
}
// Next convert the byte array to a buffered image
BufferedImage image = ((ToolkitImage) (new ImageIcon(data).getImage())).getBufferedImage();
// Is the color model something we can use?
int type = image.getType();
if (type == BufferedImage.TYPE_BYTE_BINARY || type == BufferedImage.TYPE_BYTE_GRAY) {
int w = image.getWidth();
int h = image.getHeight();
int[][] result = new int[w][h];
// obviously this could be done more efficiently
for (int i = 0; i < w; i++)
for (int j = 0; j < h; j++) result[i][j] = (image.getRGB(i, j) & 0xFF);
return result;
} else if (type == BufferedImage.TYPE_BYTE_INDEXED) {
Raster raster = image.getRaster();
if (raster.getTransferType() != DataBuffer.TYPE_BYTE) // uh oh
throw new IOException("Input Stream must contain an image with byte data if indexed.");
byte[] pixel = new byte[1];
int w = image.getWidth();
int h = image.getHeight();
int[][] result = new int[w][h];
// obviously this could be done more efficiently
for (int i = 0; i < w; i++)
for (int j = 0; j < h; j++) {
result[i][j] = ((byte[]) (raster.getDataElements(i, j, pixel)))[0];
if (result[i][j] < 0) result[i][j] += 256;
}
return result;
}
// else if (type == TYPE_USHORT_GRAY) // at present we don't handle shorts
// {
// }
else
throw new IOException(
"Input Stream must contain a binary, byte-sized grayscale, or byte-sized indexed color scheme: "
+ image);
}
public BufferedImage read(int imageIndex, ImageReadParam param) throws IOException {
checkIndex(imageIndex);
readHeader();
if (iis == null) throw new IllegalStateException("input is null");
BufferedImage img;
clearAbortRequest();
processImageStarted(imageIndex);
if (param == null) param = getDefaultReadParam();
sourceRegion = new Rectangle(0, 0, 0, 0);
destinationRegion = new Rectangle(0, 0, 0, 0);
computeRegions(
param, this.width, this.height, param.getDestination(), sourceRegion, destinationRegion);
scaleX = param.getSourceXSubsampling();
scaleY = param.getSourceYSubsampling();
// If the destination band is set used it
sourceBands = param.getSourceBands();
destBands = param.getDestinationBands();
seleBand = (sourceBands != null) && (destBands != null);
noTransform = destinationRegion.equals(new Rectangle(0, 0, width, height)) || seleBand;
if (!seleBand) {
sourceBands = new int[colorPlanes];
destBands = new int[colorPlanes];
for (int i = 0; i < colorPlanes; i++) destBands[i] = sourceBands[i] = i;
}
// If the destination is provided, then use it. Otherwise, create new one
bi = param.getDestination();
// Get the image data.
WritableRaster raster = null;
if (bi == null) {
if (sampleModel != null && colorModel != null) {
sampleModel =
sampleModel.createCompatibleSampleModel(
destinationRegion.width + destinationRegion.x,
destinationRegion.height + destinationRegion.y);
if (seleBand) sampleModel = sampleModel.createSubsetSampleModel(sourceBands);
raster = Raster.createWritableRaster(sampleModel, new Point(0, 0));
bi = new BufferedImage(colorModel, raster, false, null);
}
} else {
raster = bi.getWritableTile(0, 0);
sampleModel = bi.getSampleModel();
colorModel = bi.getColorModel();
noTransform &= destinationRegion.equals(raster.getBounds());
}
byte bdata[] = null; // buffer for byte data
if (sampleModel.getDataType() == DataBuffer.TYPE_BYTE)
bdata = (byte[]) ((DataBufferByte) raster.getDataBuffer()).getData();
readImage(bdata);
if (abortRequested()) processReadAborted();
else processImageComplete();
return bi;
}
private void writeGrayscaleImage(BufferedImage image, AVList params) throws IOException {
int type = image.getType();
int bitsPerSample =
(BufferedImage.TYPE_USHORT_GRAY == type)
? Tiff.BitsPerSample.MONOCHROME_UINT16
: Tiff.BitsPerSample.MONOCHROME_UINT8;
int numBands = image.getSampleModel().getNumBands();
// well, numBands for GrayScale images must be 1
int bytesPerSample = numBands * bitsPerSample / Byte.SIZE;
this.writeTiffHeader();
// write the image data...
int numRows = image.getHeight();
int numCols = image.getWidth();
int[] stripCounts = new int[numRows];
int[] stripOffsets = new int[numRows];
ByteBuffer dataBuff = ByteBuffer.allocateDirect(numCols * bytesPerSample);
Raster rast = image.getRaster();
for (int i = 0; i < numRows; i++) {
stripOffsets[i] = (int) this.theChannel.position();
stripCounts[i] = numCols * bytesPerSample;
int[] rowData = rast.getPixels(0, i, image.getWidth(), 1, (int[]) null);
dataBuff.clear();
if (BufferedImage.TYPE_USHORT_GRAY == type) {
for (int j = 0; j < numCols * numBands; j++) {
this.putUnsignedShort(dataBuff, rowData[j]);
}
} else if (BufferedImage.TYPE_BYTE_GRAY == type) {
for (int j = 0; j < numCols * numBands; j++) {
this.putUnsignedByte(dataBuff, rowData[j]);
}
}
dataBuff.flip();
this.theChannel.write(dataBuff);
}
// write out values for the tiff tags and build up the IFD. These are supposed to be sorted; for
// now
// do this manually here.
ArrayList<TiffIFDEntry> ifds = new ArrayList<TiffIFDEntry>(10);
ifds.add(new TiffIFDEntry(Tiff.Tag.IMAGE_WIDTH, Tiff.Type.LONG, 1, numCols));
ifds.add(new TiffIFDEntry(Tiff.Tag.IMAGE_LENGTH, Tiff.Type.LONG, 1, numRows));
ifds.add(new TiffIFDEntry(Tiff.Tag.BITS_PER_SAMPLE, Tiff.Type.SHORT, 1, bitsPerSample));
ifds.add(new TiffIFDEntry(Tiff.Tag.COMPRESSION, Tiff.Type.LONG, 1, Tiff.Compression.NONE));
ifds.add(
new TiffIFDEntry(
Tiff.Tag.PHOTO_INTERPRETATION,
Tiff.Type.SHORT,
1,
Tiff.Photometric.Grayscale_BlackIsZero));
ifds.add(
new TiffIFDEntry(Tiff.Tag.SAMPLE_FORMAT, Tiff.Type.SHORT, 1, Tiff.SampleFormat.UNSIGNED));
long offset = this.theChannel.position();
dataBuff = ByteBuffer.allocateDirect(stripOffsets.length * INTEGER_SIZEOF);
for (int stripOffset : stripOffsets) {
dataBuff.putInt(stripOffset);
}
dataBuff.flip();
this.theChannel.write(dataBuff);
ifds.add(new TiffIFDEntry(Tiff.Tag.STRIP_OFFSETS, Tiff.Type.LONG, stripOffsets.length, offset));
ifds.add(new TiffIFDEntry(Tiff.Tag.SAMPLES_PER_PIXEL, Tiff.Type.SHORT, 1, numBands));
ifds.add(new TiffIFDEntry(Tiff.Tag.ROWS_PER_STRIP, Tiff.Type.LONG, 1, 1));
offset = this.theChannel.position();
dataBuff.clear(); // stripOffsets and stripCounts are same length by design; can reuse the
// ByteBuffer...
for (int stripCount : stripCounts) {
dataBuff.putInt(stripCount);
}
dataBuff.flip();
this.theChannel.write(dataBuff);
ifds.add(
new TiffIFDEntry(Tiff.Tag.STRIP_BYTE_COUNTS, Tiff.Type.LONG, stripCounts.length, offset));
this.appendGeoTiff(ifds, params);
this.writeIFDs(ifds);
}
private void writeColorImage(BufferedImage image, AVList params) throws IOException {
int numBands = image.getRaster().getNumBands();
long offset;
this.writeTiffHeader();
// write the image data...
int numRows = image.getHeight();
int numCols = image.getWidth();
int[] stripCounts = new int[numRows];
int[] stripOffsets = new int[numRows];
ByteBuffer dataBuff = ByteBuffer.allocateDirect(numCols * numBands);
Raster rast = image.getRaster();
for (int i = 0; i < numRows; i++) {
stripOffsets[i] = (int) this.theChannel.position();
stripCounts[i] = numCols * numBands;
int[] rowData = rast.getPixels(0, i, image.getWidth(), 1, (int[]) null);
dataBuff.clear();
for (int j = 0; j < numCols * numBands; j++) {
putUnsignedByte(dataBuff, rowData[j]);
}
dataBuff.flip();
this.theChannel.write(dataBuff);
}
// write out values for the tiff tags and build up the IFD. These are supposed to be sorted; for
// now
// do this manually here.
ArrayList<TiffIFDEntry> ifds = new ArrayList<TiffIFDEntry>(10);
ifds.add(new TiffIFDEntry(Tiff.Tag.IMAGE_WIDTH, Tiff.Type.LONG, 1, numCols));
ifds.add(new TiffIFDEntry(Tiff.Tag.IMAGE_LENGTH, Tiff.Type.LONG, 1, numRows));
ifds.add(
new TiffIFDEntry(
Tiff.Tag.PLANAR_CONFIGURATION, Tiff.Type.SHORT, 1, Tiff.PlanarConfiguration.CHUNKY));
ifds.add(new TiffIFDEntry(Tiff.Tag.SAMPLES_PER_PIXEL, Tiff.Type.SHORT, 1, numBands));
ifds.add(new TiffIFDEntry(Tiff.Tag.COMPRESSION, Tiff.Type.LONG, 1, Tiff.Compression.NONE));
ifds.add(
new TiffIFDEntry(
Tiff.Tag.PHOTO_INTERPRETATION, Tiff.Type.SHORT, 1, Tiff.Photometric.Color_RGB));
ifds.add(new TiffIFDEntry(Tiff.Tag.ORIENTATION, Tiff.Type.SHORT, 1, Tiff.Orientation.DEFAULT));
offset = this.theChannel.position();
short[] bps = new short[numBands];
for (int i = 0; i < numBands; i++) {
bps[i] = Tiff.BitsPerSample.MONOCHROME_BYTE;
}
this.theChannel.write(ByteBuffer.wrap(this.getBytes(bps)));
ifds.add(new TiffIFDEntry(Tiff.Tag.BITS_PER_SAMPLE, Tiff.Type.SHORT, numBands, offset));
offset = this.theChannel.position();
dataBuff = ByteBuffer.allocateDirect(stripOffsets.length * INTEGER_SIZEOF);
for (int stripOffset : stripOffsets) {
dataBuff.putInt(stripOffset);
}
dataBuff.flip();
this.theChannel.write(dataBuff);
ifds.add(new TiffIFDEntry(Tiff.Tag.STRIP_OFFSETS, Tiff.Type.LONG, stripOffsets.length, offset));
ifds.add(new TiffIFDEntry(Tiff.Tag.ROWS_PER_STRIP, Tiff.Type.LONG, 1, 1));
offset = this.theChannel.position();
dataBuff.clear();
// stripOffsets and stripCounts are same length by design; can reuse the ByteBuffer...
for (int stripCount : stripCounts) {
dataBuff.putInt(stripCount);
}
dataBuff.flip();
this.theChannel.write(dataBuff);
ifds.add(
new TiffIFDEntry(Tiff.Tag.STRIP_BYTE_COUNTS, Tiff.Type.LONG, stripCounts.length, offset));
this.appendGeoTiff(ifds, params);
this.writeIFDs(ifds);
}