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;
}
// If defaultNewIsNull is true, then newIsNull is ignored and it should behave as
// if newIsNull were false.
private void runTest(
WritableRaster source,
double sourceNoData,
double newValue,
boolean defaultNewIsNull,
boolean newIsNull) {
ColorModel cm1 = RasterUtils.createColorModel(source);
java.util.Hashtable<String, Object> arg1Properties = new java.util.Hashtable<String, Object>();
arg1Properties.put(OpImageUtils.NODATA_PROPERTY, sourceNoData);
BufferedImage s1 = new BufferedImage(cm1, source, false, arg1Properties);
RenderedOp op = null;
if (defaultNewIsNull) {
op = ReplaceNullDescriptor.create(s1, newValue, null);
} else {
op = ReplaceNullDescriptor.create(s1, newValue, newIsNull, null);
}
Raster r = op.getData();
if (!defaultNewIsNull && newIsNull) {
Assert.assertEquals(newValue, OpImageUtils.getNoData(op, Double.NaN), EPSILON);
} else {
Assert.assertTrue(Double.isNaN(OpImageUtils.getNoData(op, Double.NaN)));
}
Assert.assertEquals(width, r.getWidth());
Assert.assertEquals(height, r.getHeight());
for (int x = 0; x < width; x++) {
for (int y = 0; y < height; y++) {
double v = r.getSampleDouble(x, y, 0);
int pixelId = getPixelId(x, y, width);
Assert.assertEquals(pixelId, v, EPSILON);
}
}
}
private Raster clipRowToRect(
final Raster raster, final Rectangle rect, final int[] bands, final int xSub) {
if (rect.contains(raster.getMinX(), 0, raster.getWidth(), 1)
&& xSub == 1
&& bands == null /* TODO: Compare bands with that of raster */) {
return raster;
}
return raster.createChild(rect.x / xSub, 0, rect.width / xSub, 1, 0, 0, bands);
}
/**
* Constructs IntegerRaster with the given size.
*
* @param _nrow the number of rows
* @param _ncol the number of columns
*/
public IntegerRaster(int _nrow, int _ncol) {
nrow = _nrow;
ncol = _ncol;
dimension = new Dimension(ncol, nrow);
int size = nrow * ncol;
ComponentColorModel ccm =
new ComponentColorModel(
ColorSpace.getInstance(ColorSpace.CS_sRGB),
new int[] {8, 8, 8},
false, // hasAlpha
false,
Transparency.OPAQUE,
DataBuffer.TYPE_BYTE);
BandedSampleModel csm =
new BandedSampleModel(
DataBuffer.TYPE_BYTE, ncol, nrow, ncol, new int[] {0, 1, 2}, new int[] {0, 0, 0});
rgbData = new byte[3][size];
DataBuffer databuffer = new DataBufferByte(rgbData, size);
WritableRaster raster = Raster.createWritableRaster(csm, databuffer, new Point(0, 0));
image = new BufferedImage(ccm, raster, false, null);
// col in x direction, row in y direction
xmin = 0;
xmax = ncol;
ymin = nrow;
ymax = 0; // zero is on top
}
// 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 final Rectangle2D getBounds2D(Raster src) {
// We position source raster to (0,0) even if it is translated child
// raster.
// This means that we need only width and height of the src
int width = src.getWidth();
int height = src.getHeight();
float[] corners = {0, 0, width, 0, width, height, 0, height};
at.transform(corners, 0, corners, 0, 4);
Rectangle2D.Float bounds = new Rectangle2D.Float(corners[0], corners[1], 0, 0);
bounds.add(corners[2], corners[3]);
bounds.add(corners[4], corners[5]);
bounds.add(corners[6], corners[7]);
return bounds;
}
@BeforeClass
public static void init() {
width = 10;
height = 10;
sm = new BandedSampleModel(DataBuffer.TYPE_DOUBLE, width, height, 1);
numbered = Raster.createWritableRaster(sm, new Point(0, 0));
numberedWithNoData = Raster.createWritableRaster(sm, new Point(0, 0));
numberedWithNanNoData = Raster.createWritableRaster(sm, new Point(0, 0));
for (int x = 0; x < width; x++) {
for (int y = 0; y < height; y++) {
int pixelId = getPixelId(x, y, width);
numbered.setSample(x, y, 0, (double) pixelId);
numberedWithNoData.setSample(
x, y, 0, ((pixelId % noDataModValue) == 0) ? NON_NAN_NODATA_VALUE : (double) pixelId);
numberedWithNanNoData.setSample(
x, y, 0, ((pixelId % noDataModValue) == 0) ? Double.NaN : (double) pixelId);
}
}
}
public WritableRaster createCompatibleDestRaster(Raster src) {
// Here approach is other then in createCompatibleDestImage -
// destination should include only
// transformed image, but not (0,0) in source coordinate system
Rectangle2D newBounds = getBounds2D(src);
return src.createCompatibleWritableRaster(
(int) newBounds.getX(),
(int) newBounds.getY(),
(int) newBounds.getWidth(),
(int) newBounds.getHeight());
}
public final WritableRaster filter(Raster src, WritableRaster dst) {
if (src == dst) {
// awt.252=Source can't be same as the destination
throw new IllegalArgumentException(Messages.getString("awt.252")); // $NON-NLS-1$
}
if (dst == null) {
dst = createCompatibleDestRaster(src);
} else if (src.getNumBands() != dst.getNumBands()) {
// awt.253=Different number of bands in source and destination
throw new IllegalArgumentException(Messages.getString("awt.253")); // $NON-NLS-1$
}
if (slowFilter(src, dst) != 0) {
// awt.21F=Unable to transform source
throw new ImagingOpException(Messages.getString("awt.21F")); // $NON-NLS-1$
// TODO - uncomment
// if (ippFilter(src, dst, BufferedImage.TYPE_CUSTOM) != 0)
// throw new ImagingOpException("Unable to transform source");
}
return dst;
}
public static BufferedImage toGrayScale(BufferedImage image) {
BufferedImage result =
new BufferedImage(image.getWidth(), image.getHeight(), BufferedImage.TYPE_BYTE_GRAY);
Raster raster = image.getData();
WritableRaster grayRaster = result.getRaster();
int height = raster.getHeight();
int sample = 0;
for (int x = 0; x < raster.getWidth(); ++x) {
for (int y = 0; y < height; ++y) {
sample = raster.getSample(x, y, 0) + raster.getSample(x, y, 1) + raster.getSample(x, y, 2);
grayRaster.setSample(x, y, 0, (int) ((float) sample / 3.0));
}
}
return result;
}
@Override
protected BufferedImage doInBackground() {
int x, y, b;
int[] A = null;
int[] sum = new int[bands], sum_x = new int[bands], sum_y = new int[bands];
WritableRaster raster = image.getRaster();
for (x = 0; x < size.getWidth(); x++) {
for (y = 0; y < size.getHeight(); y++) {
if (y == 0 || y == size.getHeight() - 1 || x == 0 || x == size.getWidth() - 1) {
for (b = 0; b < bands; b++) {
sum[b] = 0;
}
} else {
for (b = 0; b < bands; b++) {
A =
input.getSamples(
x - 1, y - 1, CSobelOperator.matrix_size, CSobelOperator.matrix_size, b, A);
sum_x[b] = CSobelOperator.getGx(A);
sum_y[b] = CSobelOperator.getGy(A);
}
for (b = 0; b < bands; b++) {
sum[b] = Math.abs(sum_x[b]) + Math.abs(sum_y[b]);
}
}
raster.setPixel(x, y, sum);
setProgress(
100
* (x * ((int) size.getHeight()) + y)
/ ((int) (size.getWidth() * size.getHeight())));
}
}
image.setData(raster);
return image;
}
public static UIFont createGuiFont(String name, int font_size) {
Font font = load_ttf(StringUtils.concat(name, ".ttf"), font_size);
UIFont tmp = new UIFont();
tmp.font_texture = new Texture();
Graphics2D graphics = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB).createGraphics();
graphics.setFont(font);
tmp.fontMetrics = graphics.getFontMetrics();
WritableRaster raster;
BufferedImage bufferedImage;
raster =
Raster.createInterleavedRaster(
DataBuffer.TYPE_BYTE,
(int) tmp.getFontImageWidth(),
(int) tmp.getFontImageHeight(),
4,
null);
bufferedImage = new BufferedImage(glAlphaColorModel, raster, false, null);
// Draw the characters on our image
Graphics2D imageGraphics = bufferedImage.createGraphics();
imageGraphics.setRenderingHint(
RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF);
imageGraphics.setRenderingHint(
RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
imageGraphics.setFont(font);
imageGraphics.setColor(Color.white.getAWTColor());
// draw every CHAR by line...
for (int i : key_table.keySet())
imageGraphics.drawString(
key_table.get(i), 0, (int) (tmp.fontMetrics.getMaxAscent() + (tmp.getHeight() * i)));
// Generate texture data
byte[] data = ((DataBufferByte) bufferedImage.getRaster().getDataBuffer()).getData();
ByteBuffer imageData = BufferUtils.create_byte_buffer(data.length);
imageData.order(ByteOrder.nativeOrder());
imageData.put(data, 0, data.length);
imageData.flip();
glBindTexture(GL_TEXTURE_2D, tmp.font_texture.id);
// Setup wrap mode
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP_TO_EDGE);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP_TO_EDGE);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_NEAREST);
glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_NEAREST);
glTexImage2D(
GL_TEXTURE_2D,
0,
GL_RGBA8,
(int) tmp.getFontImageWidth(),
(int) tmp.getFontImageHeight(),
0,
GL_RGBA,
GL_UNSIGNED_BYTE,
imageData);
return tmp;
}
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();
}
}
public BufferedImage decompress(final QuickTime.ImageDesc pDescription, final InputStream pStream)
throws IOException {
byte[] data = new byte[pDescription.dataSize];
DataInputStream stream = new DataInputStream(pStream);
try {
stream.readFully(data, 0, pDescription.dataSize);
} finally {
stream.close();
}
DataBuffer buffer = new DataBufferByte(data, data.length);
WritableRaster raster;
// TODO: Depth parameter can be 1-32 (color) or 33-40 (gray scale)
switch (pDescription.depth) {
case 40: // 8 bit gray (untested)
raster =
Raster.createInterleavedRaster(
buffer,
pDescription.width,
pDescription.height,
pDescription.width,
1,
new int[] {0},
null);
break;
case 24: // 24 bit RGB
raster =
Raster.createInterleavedRaster(
buffer,
pDescription.width,
pDescription.height,
pDescription.width * 3,
3,
new int[] {0, 1, 2},
null);
break;
case 32: // 32 bit ARGB
// WORKAROUND: There is a bug in the way Java 2D interprets the band offsets in
// Raster.createInterleavedRaster (see below) before Java 6. So, instead of
// passing a correct offset array below, we swap channel 1 & 3 to make it ABGR...
for (int y = 0; y < pDescription.height; y++) {
for (int x = 0; x < pDescription.width; x++) {
int offset = 4 * y * pDescription.width + x * 4;
byte temp = data[offset + 1];
data[offset + 1] = data[offset + 3];
data[offset + 3] = temp;
}
}
raster =
Raster.createInterleavedRaster(
buffer,
pDescription.width,
pDescription.height,
pDescription.width * 4,
4,
new int[] {3, 2, 1, 0}, // B & R mixed up. {1, 2, 3, 0} is correct
null);
break;
default:
throw new IIOException("Unsupported RAW depth: " + pDescription.depth);
}
ColorModel cm =
new ComponentColorModel(
pDescription.depth <= 32
? ColorSpace.getInstance(ColorSpace.CS_sRGB)
: ColorSpace.getInstance(ColorSpace.CS_GRAY),
pDescription.depth == 32,
false,
pDescription.depth == 32 ? Transparency.TRANSLUCENT : Transparency.OPAQUE,
DataBuffer.TYPE_BYTE);
return new BufferedImage(cm, raster, cm.isAlphaPremultiplied(), null);
}
public synchronized RenderedImage runDCRaw(dcrawMode mode, boolean secondaryPixels)
throws IOException, UnknownImageTypeException, BadImageFileException {
if (!m_decodable || (mode == dcrawMode.full && m_rawColors != 3))
throw new UnknownImageTypeException("Unsuported Camera");
RenderedImage result = null;
File of = null;
try {
if (mode == dcrawMode.preview) {
if (m_thumbWidth >= 1024 && m_thumbHeight >= 768) {
mode = dcrawMode.thumb;
}
}
long t1 = System.currentTimeMillis();
of = File.createTempFile("LZRAWTMP", ".ppm");
boolean four_colors = false;
final String makeModel = m_make + ' ' + m_model;
for (String s : four_color_cameras)
if (s.equalsIgnoreCase(makeModel)) {
four_colors = true;
break;
}
if (secondaryPixels) runDCRawInfo(true);
String cmd[];
switch (mode) {
case full:
if (four_colors)
cmd =
new String[] {
DCRAW_PATH,
"-F",
of.getAbsolutePath(),
"-v",
"-f",
"-H",
"1",
"-t",
"0",
"-o",
"0",
"-4",
m_fileName
};
else if (m_filters == -1 || (m_make != null && m_make.equalsIgnoreCase("SIGMA")))
cmd =
new String[] {
DCRAW_PATH,
"-F",
of.getAbsolutePath(),
"-v",
"-H",
"1",
"-t",
"0",
"-o",
"0",
"-4",
m_fileName
};
else if (secondaryPixels)
cmd =
new String[] {
DCRAW_PATH,
"-F",
of.getAbsolutePath(),
"-v",
"-j",
"-H",
"1",
"-t",
"0",
"-s",
"1",
"-d",
"-4",
m_fileName
};
else
cmd =
new String[] {
DCRAW_PATH,
"-F",
of.getAbsolutePath(),
"-v",
"-j",
"-H",
"1",
"-t",
"0",
"-d",
"-4",
m_fileName
};
break;
case preview:
cmd =
new String[] {
DCRAW_PATH,
"-F",
of.getAbsolutePath(),
"-v",
"-t",
"0",
"-o",
"1",
"-w",
"-h",
m_fileName
};
break;
case thumb:
cmd = new String[] {DCRAW_PATH, "-F", of.getAbsolutePath(), "-v", "-e", m_fileName};
break;
default:
throw new IllegalArgumentException("Unknown mode " + mode);
}
String ofName = null;
synchronized (DCRaw.class) {
Process p = null;
InputStream dcrawStdErr;
InputStream dcrawStdOut;
if (ForkDaemon.INSTANCE != null) {
ForkDaemon.INSTANCE.invoke(cmd);
dcrawStdErr = ForkDaemon.INSTANCE.getStdErr();
dcrawStdOut = ForkDaemon.INSTANCE.getStdOut();
} else {
p = Runtime.getRuntime().exec(cmd);
dcrawStdErr = new BufferedInputStream(p.getErrorStream());
dcrawStdOut = p.getInputStream();
}
String line, args;
// output expected on stderr
while ((line = readln(dcrawStdErr)) != null) {
// System.out.println(line);
if ((args = match(line, DCRAW_OUTPUT)) != null)
ofName = args.substring(0, args.indexOf(" ..."));
}
// Flush stdout just in case...
while ((line = readln(dcrawStdOut)) != null) ; // System.out.println(line);
if (p != null) {
dcrawStdErr.close();
try {
p.waitFor();
} catch (InterruptedException e) {
e.printStackTrace();
}
m_error = p.exitValue();
p.destroy();
} else m_error = 0;
}
System.out.println("dcraw value: " + m_error);
if (m_error > 0) {
of.delete();
throw new BadImageFileException(of);
}
if (!ofName.equals(of.getPath())) {
of.delete();
of = new File(ofName);
}
if (of.getName().endsWith(".jpg") || of.getName().endsWith(".tiff")) {
if (of.getName().endsWith(".jpg")) {
try {
LCJPEGReader jpegReader = new LCJPEGReader(of.getPath());
result = jpegReader.getImage();
} catch (Exception e) {
e.printStackTrace();
}
} else {
try {
LCTIFFReader tiffReader = new LCTIFFReader(of.getPath());
result = tiffReader.getImage(null);
} catch (Exception e) {
e.printStackTrace();
}
}
long t2 = System.currentTimeMillis();
int totalData =
result.getWidth()
* result.getHeight()
* result.getColorModel().getNumColorComponents()
* (result.getColorModel().getTransferType() == DataBuffer.TYPE_BYTE ? 1 : 2);
System.out.println("Read " + totalData + " bytes in " + (t2 - t1) + "ms");
} else {
ImageData imageData;
try {
imageData = readPPM(of);
} catch (Exception e) {
e.printStackTrace();
throw new BadImageFileException(of, e);
}
// do not change the initial image geometry
// m_width = Math.min(m_width, imageData.width);
// m_height = Math.min(m_height, imageData.height);
long t2 = System.currentTimeMillis();
int totalData =
imageData.width
* imageData.height
* imageData.bands
* (imageData.dataType == DataBuffer.TYPE_BYTE ? 1 : 2);
System.out.println("Read " + totalData + " bytes in " + (t2 - t1) + "ms");
final ColorModel cm;
if (mode == dcrawMode.full) {
if (imageData.bands == 1) {
cm =
new ComponentColorModel(
ColorSpace.getInstance(ColorSpace.CS_GRAY),
false,
false,
Transparency.OPAQUE,
DataBuffer.TYPE_USHORT);
} else {
cm = JAIContext.colorModel_linear16;
}
} else {
if (imageData.bands == 3)
cm =
new ComponentColorModel(
JAIContext.sRGBColorSpace,
false,
false,
Transparency.OPAQUE,
DataBuffer.TYPE_BYTE);
else if (imageData.bands == 4)
cm =
new ComponentColorModel(
JAIContext.CMYKColorSpace,
false,
false,
Transparency.OPAQUE,
imageData.dataType);
else throw new UnknownImageTypeException("Weird number of bands: " + imageData.bands);
}
final DataBuffer buf =
imageData.dataType == DataBuffer.TYPE_BYTE
? new DataBufferByte(
(byte[]) imageData.data, imageData.bands * imageData.width * imageData.height)
: new DataBufferUShort(
(short[]) imageData.data, imageData.bands * imageData.width * imageData.height);
final WritableRaster raster =
Raster.createInterleavedRaster(
buf,
imageData.width,
imageData.height,
imageData.bands * imageData.width,
imageData.bands,
imageData.bands == 3 ? new int[] {0, 1, 2} : new int[] {0},
null);
result = new BufferedImage(cm, raster, false, null);
}
} catch (IOException e) {
if (of != null) of.delete();
throw e;
} finally {
if (of != null) of.delete();
}
return result;
}
/**
* Slow filter.
*
* @param src the src.
* @param dst the dst.
* @return the int.
*/
private int slowFilter(Raster src, WritableRaster dst) {
// TODO: make correct interpolation
// TODO: what if there are different data types?
Rectangle srcBounds = src.getBounds();
Rectangle dstBounds = dst.getBounds();
Rectangle normDstBounds = new Rectangle(0, 0, dstBounds.width, dstBounds.height);
Rectangle bounds = getBounds2D(src).getBounds().intersection(normDstBounds);
AffineTransform inv = null;
try {
inv = at.createInverse();
} catch (NoninvertibleTransformException e) {
return -1;
}
double[] m = new double[6];
inv.getMatrix(m);
int minSrcX = srcBounds.x;
int minSrcY = srcBounds.y;
int maxSrcX = srcBounds.x + srcBounds.width;
int maxSrcY = srcBounds.y + srcBounds.height;
int minX = bounds.x + dstBounds.x;
int minY = bounds.y + dstBounds.y;
int maxX = minX + bounds.width;
int maxY = minY + bounds.height;
int hx = (int) (m[0] * 256);
int hy = (int) (m[1] * 256);
int vx = (int) (m[2] * 256);
int vy = (int) (m[3] * 256);
int sx = (int) (m[4] * 256) + hx * bounds.x + vx * bounds.y + (srcBounds.x) * 256;
int sy = (int) (m[5] * 256) + hy * bounds.x + vy * bounds.y + (srcBounds.y) * 256;
vx -= hx * bounds.width;
vy -= hy * bounds.width;
if (src.getTransferType() == dst.getTransferType()) {
for (int y = minY; y < maxY; y++) {
for (int x = minX; x < maxX; x++) {
int px = sx >> 8;
int py = sy >> 8;
if (px >= minSrcX && py >= minSrcY && px < maxSrcX && py < maxSrcY) {
Object val = src.getDataElements(px, py, null);
dst.setDataElements(x, y, val);
}
sx += hx;
sy += hy;
}
sx += vx;
sy += vy;
}
} else {
float pixel[] = null;
for (int y = minY; y < maxY; y++) {
for (int x = minX; x < maxX; x++) {
int px = sx >> 8;
int py = sy >> 8;
if (px >= minSrcX && py >= minSrcY && px < maxSrcX && py < maxSrcY) {
pixel = src.getPixel(px, py, pixel);
dst.setPixel(x, y, pixel);
}
sx += hx;
sy += hy;
}
sx += vx;
sy += vy;
}
}
return 0;
}
/**
* Ipp filter.
*
* @param src the src.
* @param dst the dst.
* @param imageType the image type.
* @return the int.
*/
@SuppressWarnings("unused")
private int ippFilter(Raster src, WritableRaster dst, int imageType) {
int srcStride, dstStride;
boolean skipChannel = false;
int channels;
int offsets[] = null;
switch (imageType) {
case BufferedImage.TYPE_INT_RGB:
case BufferedImage.TYPE_INT_BGR:
{
channels = 4;
srcStride = src.getWidth() * 4;
dstStride = dst.getWidth() * 4;
skipChannel = true;
break;
}
case BufferedImage.TYPE_INT_ARGB:
case BufferedImage.TYPE_INT_ARGB_PRE:
case BufferedImage.TYPE_4BYTE_ABGR:
case BufferedImage.TYPE_4BYTE_ABGR_PRE:
{
channels = 4;
srcStride = src.getWidth() * 4;
dstStride = dst.getWidth() * 4;
break;
}
case BufferedImage.TYPE_BYTE_GRAY:
case BufferedImage.TYPE_BYTE_INDEXED:
{
channels = 1;
srcStride = src.getWidth();
dstStride = dst.getWidth();
break;
}
case BufferedImage.TYPE_3BYTE_BGR:
{
channels = 3;
srcStride = src.getWidth() * 3;
dstStride = dst.getWidth() * 3;
break;
}
case BufferedImage.TYPE_USHORT_GRAY: // TODO - could be done in
// native code?
case BufferedImage.TYPE_USHORT_565_RGB:
case BufferedImage.TYPE_USHORT_555_RGB:
case BufferedImage.TYPE_BYTE_BINARY:
{
return slowFilter(src, dst);
}
default:
{
SampleModel srcSM = src.getSampleModel();
SampleModel dstSM = dst.getSampleModel();
if (srcSM instanceof PixelInterleavedSampleModel
&& dstSM instanceof PixelInterleavedSampleModel) {
// Check PixelInterleavedSampleModel
if (srcSM.getDataType() != DataBuffer.TYPE_BYTE
|| dstSM.getDataType() != DataBuffer.TYPE_BYTE) {
return slowFilter(src, dst);
}
channels = srcSM.getNumBands(); // Have IPP functions for 1,
// 3 and 4 channels
if (channels != 1 && channels != 3 && channels != 4) {
return slowFilter(src, dst);
}
int dataTypeSize = DataBuffer.getDataTypeSize(srcSM.getDataType()) / 8;
srcStride = ((ComponentSampleModel) srcSM).getScanlineStride() * dataTypeSize;
dstStride = ((ComponentSampleModel) dstSM).getScanlineStride() * dataTypeSize;
} else if (srcSM instanceof SinglePixelPackedSampleModel
&& dstSM instanceof SinglePixelPackedSampleModel) {
// Check SinglePixelPackedSampleModel
SinglePixelPackedSampleModel sppsm1 = (SinglePixelPackedSampleModel) srcSM;
SinglePixelPackedSampleModel sppsm2 = (SinglePixelPackedSampleModel) dstSM;
// No IPP function for this type
if (sppsm1.getDataType() == DataBuffer.TYPE_USHORT) {
return slowFilter(src, dst);
}
channels = sppsm1.getNumBands();
// Have IPP functions for 1, 3 and 4 channels
if (channels != 1 && channels != 3 && channels != 4) {
return slowFilter(src, dst);
}
// Check compatibility of sample models
if (sppsm1.getDataType() != sppsm2.getDataType()
|| !Arrays.equals(sppsm1.getBitOffsets(), sppsm2.getBitOffsets())
|| !Arrays.equals(sppsm1.getBitMasks(), sppsm2.getBitMasks())) {
return slowFilter(src, dst);
}
for (int i = 0; i < channels; i++) {
if (sppsm1.getSampleSize(i) != 8) {
return slowFilter(src, dst);
}
}
if (channels == 3) {
channels = 4;
}
int dataTypeSize = DataBuffer.getDataTypeSize(sppsm1.getDataType()) / 8;
srcStride = sppsm1.getScanlineStride() * dataTypeSize;
dstStride = sppsm2.getScanlineStride() * dataTypeSize;
} else {
return slowFilter(src, dst);
}
// Fill offsets if there's a child raster
if (src.getParent() != null || dst.getParent() != null) {
if (src.getSampleModelTranslateX() != 0
|| src.getSampleModelTranslateY() != 0
|| dst.getSampleModelTranslateX() != 0
|| dst.getSampleModelTranslateY() != 0) {
offsets = new int[4];
offsets[0] = -src.getSampleModelTranslateX() + src.getMinX();
offsets[1] = -src.getSampleModelTranslateY() + src.getMinY();
offsets[2] = -dst.getSampleModelTranslateX() + dst.getMinX();
offsets[3] = -dst.getSampleModelTranslateY() + dst.getMinY();
}
}
}
}
double m00 = at.getScaleX();
double m01 = at.getShearX();
double m02 = at.getTranslateX();
double m10 = at.getShearY();
double m11 = at.getScaleY();
double m12 = at.getTranslateY();
Object srcData, dstData;
AwtImageBackdoorAccessor dbAccess = AwtImageBackdoorAccessor.getInstance();
try {
srcData = dbAccess.getData(src.getDataBuffer());
dstData = dbAccess.getData(dst.getDataBuffer());
} catch (IllegalArgumentException e) {
return -1; // Unknown data buffer type
}
return ippAffineTransform(
m00,
m01,
m02,
m10,
m11,
m12,
srcData,
src.getWidth(),
src.getHeight(),
srcStride,
dstData,
dst.getWidth(),
dst.getHeight(),
dstStride,
iType,
channels,
skipChannel,
offsets);
}
/** 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 Raster getRaster(int x, int y, int w, int h) {
return Raster.createBandedRaster(0, 0, 0, 0, NULL_POINT);
}
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;
}
/**
* Paint the image onto a Graphics object. The painting is performed tile-by-tile, and includes a
* grey region covering the unused portion of image tiles as well as the general background. At
* this point the image must be byte data.
*/
public synchronized void paintComponent(Graphics g) {
Graphics2D g2D = null;
if (g instanceof Graphics2D) {
g2D = (Graphics2D) g;
} else {
return;
}
// if source is null, it's just a component
if (source == null) {
g2D.setColor(getBackground());
g2D.fillRect(0, 0, componentWidth, componentHeight);
return;
}
int transX = -originX;
int transY = -originY;
// Get the clipping rectangle and translate it into image coordinates.
Rectangle clipBounds = g.getClipBounds();
if (clipBounds == null) {
clipBounds = new Rectangle(0, 0, componentWidth, componentHeight);
}
// clear the background (clip it) [minimal optimization here]
if (transX > 0
|| transY > 0
|| transX < (componentWidth - source.getWidth())
|| transY < (componentHeight - source.getHeight())) {
g2D.setColor(getBackground());
g2D.fillRect(0, 0, componentWidth, componentHeight);
}
clipBounds.translate(-transX, -transY);
// Determine the extent of the clipping region in tile coordinates.
int txmin, txmax, tymin, tymax;
int ti, tj;
txmin = XtoTileX(clipBounds.x);
txmin = Math.max(txmin, minTileX);
txmin = Math.min(txmin, maxTileX);
txmax = XtoTileX(clipBounds.x + clipBounds.width - 1);
txmax = Math.max(txmax, minTileX);
txmax = Math.min(txmax, maxTileX);
tymin = YtoTileY(clipBounds.y);
tymin = Math.max(tymin, minTileY);
tymin = Math.min(tymin, maxTileY);
tymax = YtoTileY(clipBounds.y + clipBounds.height - 1);
tymax = Math.max(tymax, minTileY);
tymax = Math.min(tymax, maxTileY);
Insets insets = getInsets();
// Loop over tiles within the clipping region
for (tj = tymin; tj <= tymax; tj++) {
for (ti = txmin; ti <= txmax; ti++) {
int tx = TileXtoX(ti);
int ty = TileYtoY(tj);
Raster tile = source.getTile(ti, tj);
if (tile != null) {
DataBuffer dataBuffer = tile.getDataBuffer();
WritableRaster wr = tile.createWritableRaster(sampleModel, dataBuffer, null);
BufferedImage bi =
new BufferedImage(colorModel, wr, colorModel.isAlphaPremultiplied(), null);
// correctly handles band offsets
if (brightnessEnabled == true) {
SampleModel sm =
sampleModel.createCompatibleSampleModel(tile.getWidth(), tile.getHeight());
WritableRaster raster = RasterFactory.createWritableRaster(sm, null);
BufferedImage bimg =
new BufferedImage(colorModel, raster, colorModel.isAlphaPremultiplied(), null);
// don't move this code
ByteLookupTable lutTable = new ByteLookupTable(0, lutData);
LookupOp lookup = new LookupOp(lutTable, null);
lookup.filter(bi, bimg);
g2D.drawImage(bimg, biop, tx + transX + insets.left, ty + transY + insets.top);
} else {
AffineTransform transform;
transform =
AffineTransform.getTranslateInstance(
tx + transX + insets.left, ty + transY + insets.top);
g2D.drawRenderedImage(bi, transform);
}
}
}
}
}
@Override
public BufferedImage read(final int imageIndex, final ImageReadParam param) throws IOException {
Iterator<ImageTypeSpecifier> imageTypes = getImageTypes(imageIndex);
ImageTypeSpecifier rawType = getRawImageType(imageIndex);
if (header.getPaletteInfo() != PCX.PALETTEINFO_COLOR
&& header.getPaletteInfo() != PCX.PALETTEINFO_GRAY) {
processWarningOccurred(
String.format(
"Unsupported color mode: %d, colors may look incorrect", header.getPaletteInfo()));
}
int width = getWidth(imageIndex);
int height = getHeight(imageIndex);
BufferedImage destination = getDestination(param, imageTypes, width, height);
Rectangle srcRegion = new Rectangle();
Rectangle destRegion = new Rectangle();
computeRegions(param, width, height, destination, srcRegion, destRegion);
WritableRaster destRaster =
clipToRect(
destination.getRaster(),
destRegion,
param != null ? param.getDestinationBands() : null);
checkReadParamBandSettings(param, rawType.getNumBands(), destRaster.getNumBands());
int compression = header.getCompression();
// Wrap input (COMPRESSION_RLE is really the only value allowed)
DataInput input =
compression == PCX.COMPRESSION_RLE
? new DataInputStream(
new DecoderStream(IIOUtil.createStreamAdapter(imageInput), new RLEDecoder()))
: imageInput;
int xSub = param != null ? param.getSourceXSubsampling() : 1;
int ySub = param != null ? param.getSourceYSubsampling() : 1;
processImageStarted(imageIndex);
if (rawType.getColorModel() instanceof IndexColorModel && header.getChannels() > 1) {
// Bit planes!
// Create raster from a default 8 bit layout
WritableRaster rowRaster = GRAYSCALE.createBufferedImage(header.getWidth(), 1).getRaster();
// Clip to source region
Raster clippedRow =
clipRowToRect(
rowRaster,
srcRegion,
param != null ? param.getSourceBands() : null,
param != null ? param.getSourceXSubsampling() : 1);
int planeWidth = header.getBytesPerLine();
byte[] planeData = new byte[planeWidth * 8];
byte[] rowDataByte = ((DataBufferByte) rowRaster.getDataBuffer()).getData();
for (int y = 0; y < height; y++) {
switch (header.getBitsPerPixel()) {
case 1:
readRowByte(
input,
srcRegion,
xSub,
ySub,
planeData,
0,
planeWidth * header.getChannels(),
destRaster,
clippedRow,
y);
break;
default:
throw new AssertionError();
}
int pixelPos = 0;
for (int planePos = 0; planePos < planeWidth; planePos++) {
BitRotator.bitRotateCW(planeData, planePos, planeWidth, rowDataByte, pixelPos, 1);
pixelPos += 8;
}
processImageProgress(100f * y / height);
if (y >= srcRegion.y + srcRegion.height) {
break;
}
if (abortRequested()) {
processReadAborted();
break;
}
}
} else if (header.getBitsPerPixel() == 24 || header.getBitsPerPixel() == 32) {
// Can't use width here, as we need to take bytesPerLine into account, and re-create a width
// based on this
int rowWidth = (header.getBytesPerLine() * 8) / header.getBitsPerPixel();
WritableRaster rowRaster = rawType.createBufferedImage(rowWidth, 1).getRaster();
// Clip to source region
Raster clippedRow =
clipRowToRect(
rowRaster,
srcRegion,
param != null ? param.getSourceBands() : null,
param != null ? param.getSourceXSubsampling() : 1);
for (int y = 0; y < height; y++) {
byte[] rowDataByte = ((DataBufferByte) rowRaster.getDataBuffer()).getData();
readRowByte(
input,
srcRegion,
xSub,
ySub,
rowDataByte,
0,
rowDataByte.length,
destRaster,
clippedRow,
y);
processImageProgress(100f * y / height);
if (y >= srcRegion.y + srcRegion.height) {
break;
}
if (abortRequested()) {
processReadAborted();
break;
}
}
} else {
// Can't use width here, as we need to take bytesPerLine into account, and re-create a width
// based on this
int rowWidth = (header.getBytesPerLine() * 8) / header.getBitsPerPixel();
WritableRaster rowRaster = rawType.createBufferedImage(rowWidth, 1).getRaster();
// Clip to source region
Raster clippedRow =
clipRowToRect(
rowRaster,
srcRegion,
param != null ? param.getSourceBands() : null,
param != null ? param.getSourceXSubsampling() : 1);
for (int y = 0; y < height; y++) {
for (int c = 0; c < header.getChannels(); c++) {
WritableRaster destChannel =
destRaster.createWritableChild(
destRaster.getMinX(),
destRaster.getMinY(),
destRaster.getWidth(),
destRaster.getHeight(),
0,
0,
new int[] {c});
Raster srcChannel =
clippedRow.createChild(
clippedRow.getMinX(), 0, clippedRow.getWidth(), 1, 0, 0, new int[] {c});
switch (header.getBitsPerPixel()) {
case 1:
case 2:
case 4:
case 8:
byte[] rowDataByte = ((DataBufferByte) rowRaster.getDataBuffer()).getData(c);
readRowByte(
input,
srcRegion,
xSub,
ySub,
rowDataByte,
0,
rowDataByte.length,
destChannel,
srcChannel,
y);
break;
default:
throw new AssertionError();
}
if (abortRequested()) {
break;
}
}
processImageProgress(100f * y / height);
if (y >= srcRegion.y + srcRegion.height) {
break;
}
if (abortRequested()) {
processReadAborted();
break;
}
}
}
processImageComplete();
return destination;
}