private void writePixels(String chunk, byte[] stream, int x, int y, int width, int height)
throws FormatException, IOException {
MetadataRetrieve r = getMetadataRetrieve();
int sizeC = getSamplesPerPixel();
String type = r.getPixelsType(series).toString();
int pixelType = FormatTools.pixelTypeFromString(type);
boolean signed = FormatTools.isSigned(pixelType);
if (!isFullPlane(x, y, width, height)) {
throw new FormatException("APNGWriter does not support writing tiles.");
}
ByteArrayOutputStream s = new ByteArrayOutputStream();
s.write(chunk.getBytes());
if (chunk.equals("fdAT")) {
s.write(DataTools.intToBytes(nextSequenceNumber++, false));
}
DeflaterOutputStream deflater = new DeflaterOutputStream(s);
int planeSize = stream.length / sizeC;
int rowLen = stream.length / height;
int bytesPerPixel = stream.length / (width * height * sizeC);
byte[] rowBuf = new byte[rowLen];
for (int i = 0; i < height; i++) {
deflater.write(0);
if (interleaved) {
if (littleEndian) {
for (int col = 0; col < width * sizeC; col++) {
int offset = (i * sizeC * width + col) * bytesPerPixel;
int pixel = DataTools.bytesToInt(stream, offset, bytesPerPixel, littleEndian);
DataTools.unpackBytes(pixel, rowBuf, col * bytesPerPixel, bytesPerPixel, false);
}
} else System.arraycopy(stream, i * rowLen, rowBuf, 0, rowLen);
} else {
int max = (int) Math.pow(2, bytesPerPixel * 8 - 1);
for (int col = 0; col < width; col++) {
for (int c = 0; c < sizeC; c++) {
int offset = c * planeSize + (i * width + col) * bytesPerPixel;
int pixel = DataTools.bytesToInt(stream, offset, bytesPerPixel, littleEndian);
if (signed) {
if (pixel < max) pixel += max;
else pixel -= max;
}
int output = (col * sizeC + c) * bytesPerPixel;
DataTools.unpackBytes(pixel, rowBuf, output, bytesPerPixel, false);
}
}
}
deflater.write(rowBuf);
}
deflater.finish();
byte[] b = s.toByteArray();
// write chunk length
out.writeInt(b.length - 4);
out.write(b);
// write checksum
out.writeInt(crc(b));
}
/** @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int) */
public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException {
checkParams(no, buf, x, y, w, h);
MetadataRetrieve meta = getMetadataRetrieve();
int sizeX = meta.getPixelsSizeX(series).getValue().intValue();
int nChannels = getSamplesPerPixel();
// write pixel data
// for simplicity, write 80 char lines
if (!initialized[series][no]) {
initialized[series][no] = true;
writeHeader();
if (!isFullPlane(x, y, w, h)) {
// write a dummy plane that will be overwritten in sections
int planeSize = w * h * nChannels;
for (int i = 0; i < planeSize; i++) {
out.writeBytes(DUMMY_PIXEL);
}
}
}
int planeSize = w * h;
StringBuffer buffer = new StringBuffer();
int offset = y * sizeX * nChannels * 2;
out.seek(planeOffset + offset);
for (int row = 0; row < h; row++) {
out.skipBytes(nChannels * x * 2);
for (int col = 0; col < w * nChannels; col++) {
int i = row * w * nChannels + col;
int index =
interleaved || nChannels == 1 ? i : (i % nChannels) * planeSize + (i / nChannels);
String s = Integer.toHexString(buf[index]);
// only want last 2 characters of s
if (s.length() > 1) buffer.append(s.substring(s.length() - 2));
else {
buffer.append("0");
buffer.append(s);
}
}
out.writeBytes(buffer.toString());
buffer.delete(0, buffer.length());
out.skipBytes(nChannels * (sizeX - w - x) * 2);
}
// write footer
out.seek(out.length());
out.writeBytes("\nshowpage\n");
}
/* @see loci.formats.IFormatHandler#setId(String) */
public void setId(String id) throws FormatException, IOException {
super.setId(id);
if (out.length() == 0) {
MetadataRetrieve r = getMetadataRetrieve();
int width = r.getPixelsSizeX(series).getValue().intValue();
int height = r.getPixelsSizeY(series).getValue().intValue();
int bytesPerPixel = FormatTools.getBytesPerPixel(r.getPixelsType(series).toString());
int nChannels = getSamplesPerPixel();
boolean indexed = getColorModel() != null && (getColorModel() instanceof IndexColorModel);
littleEndian = !r.getPixelsBinDataBigEndian(series, 0);
// write 8-byte PNG signature
out.write(PNG_SIG);
// write IHDR chunk
out.writeInt(13);
byte[] b = new byte[17];
b[0] = 'I';
b[1] = 'H';
b[2] = 'D';
b[3] = 'R';
DataTools.unpackBytes(width, b, 4, 4, false);
DataTools.unpackBytes(height, b, 8, 4, false);
b[12] = (byte) (bytesPerPixel * 8);
if (indexed) b[13] = (byte) 3;
else if (nChannels == 1) b[13] = (byte) 0;
else if (nChannels == 2) b[13] = (byte) 4;
else if (nChannels == 3) b[13] = (byte) 2;
else if (nChannels == 4) b[13] = (byte) 6;
b[14] = (byte) 0;
b[15] = (byte) 0;
b[16] = (byte) 0;
out.write(b);
out.writeInt(crc(b));
// write acTL chunk
out.writeInt(8);
out.writeBytes("acTL");
numFramesPointer = out.getFilePointer();
out.writeInt(0);
out.writeInt(0);
out.writeInt(0); // save a place for the CRC
}
}
/** @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int) */
public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException {
checkParams(no, buf, x, y, w, h);
if (!isFullPlane(x, y, w, h)) {
throw new FormatException("APNGWriter does not yet support saving image tiles.");
}
MetadataRetrieve meta = getMetadataRetrieve();
int width = meta.getPixelsSizeX(series).getValue().intValue();
int height = meta.getPixelsSizeY(series).getValue().intValue();
if (!initialized[series][no]) {
writeFCTL(width, height);
if (numFrames == 0) writePLTE();
initialized[series][no] = true;
}
writePixels(numFrames == 0 ? "IDAT" : "fdAT", buf, x, y, w, h);
numFrames++;
}
private void writeHeader() throws IOException {
MetadataRetrieve r = getMetadataRetrieve();
int width = r.getPixelsSizeX(series).getValue().intValue();
int height = r.getPixelsSizeY(series).getValue().intValue();
int nChannels = getSamplesPerPixel();
out.writeBytes("%!PS-Adobe-2.0 EPSF-1.2\n");
out.writeBytes("%%Title: " + currentId + "\n");
out.writeBytes("%%Creator: OME Bio-Formats\n");
out.writeBytes("%%Pages: 1\n");
out.writeBytes("%%BoundingBox: 0 0 " + width + " " + height + "\n");
out.writeBytes("%%EndComments\n\n");
out.writeBytes("/ld {load def} bind def\n");
out.writeBytes(
"/s /stroke ld /f /fill ld /m /moveto ld /l "
+ "/lineto ld /c /curveto ld /rgb {255 div 3 1 roll 255 div 3 1 "
+ "roll 255 div 3 1 roll setrgbcolor} def\n");
out.writeBytes("0 0 translate\n");
out.writeBytes(((float) width) + " " + ((float) height) + " scale\n");
out.writeBytes("/picstr 40 string def\n");
out.writeBytes(
width
+ " "
+ height
+ " 8 ["
+ width
+ " 0 0 "
+ (-1 * height)
+ " 0 "
+ height
+ "] {currentfile picstr readhexstring pop} ");
if (nChannels == 1) {
out.writeBytes("image\n");
} else {
out.writeBytes("false 3 colorimage\n");
}
planeOffset = out.getFilePointer();
}
/** Retrieves calibration for X,Y,Z,T * */
private float[] getCalibration(final IFormatReader r, final int[] dimensions) {
float[] calibration = new float[dimensions.length];
for (int i = 0; i < calibration.length; ++i) calibration[i] = 1;
try {
final String dimOrder = r.getDimensionOrder().toUpperCase();
final MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore();
PositiveFloat cal;
final int posX = dimOrder.indexOf('X');
cal = retrieve.getPixelsPhysicalSizeX(0);
if (posX >= 0 && posX < calibration.length && cal != null && cal.getValue() != 0)
calibration[posX] = cal.getValue().floatValue();
final int posY = dimOrder.indexOf('Y');
cal = retrieve.getPixelsPhysicalSizeY(0);
if (posY >= 0 && posY < calibration.length && cal != null && cal.getValue() != 0)
calibration[posY] = cal.getValue().floatValue();
final int posZ = dimOrder.indexOf('Z');
cal = retrieve.getPixelsPhysicalSizeZ(0);
if (posZ >= 0 && posZ < calibration.length && cal != null && cal.getValue() != 0)
calibration[posZ] = cal.getValue().floatValue();
final int posT = dimOrder.indexOf('T');
retrieve.getPixelsTimeIncrement(0);
Double cal1 = retrieve.getPixelsTimeIncrement(0);
if (posT >= 0 && posT < calibration.length && cal1 != null && cal1.floatValue() != 0)
calibration[posT] = cal1.floatValue();
} catch (Exception e) {
// somehow an error occured reading the calibration
}
return calibration;
}
public static double[] readImageInfo(String id) {
try {
reader.setId(id);
} catch (FormatException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
// ORDERING: 0 little, 1 seriesCount, 2 pixelType, 3 bpp, 4 itkComponentType, 5 sizeX,
// 6 sizeY, 7 sizeZ, 8 sizeT, 9 sizeC, 10 effSizeC, 11 rgbChannelCount, 12 imageCount
// 13 physX, 14 physY, 15 physZ, 16 timeIncrement
double[] returnValues = new double[17];
// return this and use SetByteOrderToLittleEndian or SetByteOrderToBigEndian in C++ land
boolean little = reader.isLittleEndian();
if (little) {
returnValues[0] = 1;
} else {
returnValues[0] = 0;
}
returnValues[1] = reader.getSeriesCount();
// return bpp and set an IOComponent based on it
int pixelType = reader.getPixelType();
returnValues[2] = (double) pixelType;
returnValues[3] = (double) FormatTools.getBytesPerPixel((int) returnValues[2]);
// 0 UCHAR, 1 CHAR, 2 USHORT, 3 SHORT, 4 UINT, 5 INT, 6 FLOAT, 7 DOUBLE, 8 UNKNOWN
if (pixelType == FormatTools.UINT8) returnValues[4] = (double) 0;
else if (pixelType == FormatTools.INT8) returnValues[4] = (double) 1;
else if (pixelType == FormatTools.UINT16) returnValues[4] = (double) 2;
else if (pixelType == FormatTools.INT16) returnValues[4] = (double) 3;
else if (pixelType == FormatTools.UINT32) returnValues[4] = (double) 4;
else if (pixelType == FormatTools.INT32) returnValues[4] = (double) 5;
else if (pixelType == FormatTools.FLOAT) returnValues[4] = (double) 6;
else if (pixelType == FormatTools.DOUBLE) returnValues[4] = (double) 7;
else returnValues[4] = (double) 8;
// return these
returnValues[5] = (double) reader.getSizeX();
returnValues[6] = (double) reader.getSizeY();
returnValues[7] = (double) reader.getSizeZ();
returnValues[8] = (double) reader.getSizeT();
returnValues[9] = (double) reader.getSizeC();
returnValues[10] = (double) reader.getEffectiveSizeC();
returnValues[11] = (double) reader.getRGBChannelCount();
returnValues[12] = (double) reader.getImageCount();
MetadataRetrieve retrieve = MetadataTools.asRetrieve(reader.getMetadataStore());
Double d = retrieve.getPixelsPhysicalSizeX(0).getValue();
double d2 = d == null ? 1.0 : d.doubleValue();
returnValues[13] = d2;
d = retrieve.getPixelsPhysicalSizeY(0).getValue();
d2 = d == null ? 1.0 : d.doubleValue();
returnValues[14] = d2;
d = retrieve.getPixelsPhysicalSizeZ(0).getValue();
d2 = d == null ? 1.0 : d.doubleValue();
returnValues[15] = d2;
d = retrieve.getPixelsTimeIncrement(0);
d2 = d == null ? 1.0 : d.doubleValue();
returnValues[16] = d2;
return returnValues;
}