Esempio n. 1
0
  /** @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int) */
  public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
      throws FormatException, IOException {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);

    long planeSize = FormatTools.getPlaneSize(this);
    long offset = HEADER_SIZE + extHeaderSize + no * planeSize;

    if (offset + planeSize <= in.length() && offset >= 0) {
      in.seek(offset);
      readPlane(in, x, getSizeY() - h - y, w, h, buf);

      // reverse the order of the rows
      // planes are stored with the origin in the lower-left corner
      byte[] tmp = new byte[w * FormatTools.getBytesPerPixel(getPixelType())];
      for (int row = 0; row < h / 2; row++) {
        int src = row * tmp.length;
        int dest = (h - row - 1) * tmp.length;
        System.arraycopy(buf, src, tmp, 0, tmp.length);
        System.arraycopy(buf, dest, buf, src, tmp.length);
        System.arraycopy(tmp, 0, buf, dest, tmp.length);
      }
    }

    return buf;
  }
  /** @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int) */
  public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
      throws FormatException, IOException {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);

    if (getCoreIndex() < core.length - ifds.size()) {
      int tileRows = rows[getCoreIndex()];
      int tileCols = cols[getCoreIndex()];

      Region image = new Region(x, y, w, h);
      int outputRow = 0, outputCol = 0;
      Region intersection = null;

      byte[] tileBuf = null;
      int pixel = getRGBChannelCount() * FormatTools.getBytesPerPixel(getPixelType());
      int outputRowLen = w * pixel;

      for (int row = 0; row < tileRows; row++) {
        for (int col = 0; col < tileCols; col++) {
          int width = tileX[getCoreIndex()];
          int height = tileY[getCoreIndex()];
          Region tile = new Region(col * width, row * height, width, height);
          if (!tile.intersects(image)) {
            continue;
          }

          intersection = tile.intersection(image);
          int intersectionX = 0;

          if (tile.x < image.x) {
            intersectionX = image.x - tile.x;
          }

          tileBuf = decodeTile(no, row, col);

          int rowLen = pixel * (int) Math.min(intersection.width, width);

          int outputOffset = outputRow * outputRowLen + outputCol;
          for (int trow = 0; trow < intersection.height; trow++) {
            int realRow = trow + intersection.y - tile.y;
            int inputOffset = pixel * (realRow * width + intersectionX);
            System.arraycopy(tileBuf, inputOffset, buf, outputOffset, rowLen);
            outputOffset += outputRowLen;
          }

          outputCol += rowLen;
        }

        if (intersection != null) {
          outputRow += intersection.height;
          outputCol = 0;
        }
      }

      return buf;
    } else {
      int ifdIndex = getCoreIndex() - (usedFiles.length - 1);
      return parser.getSamples(ifds.get(ifdIndex), buf, x, y, w, h);
    }
  }
  /** @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int) */
  public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
      throws FormatException, IOException {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    if (getSizeC() == 1) {
      return super.openBytes(no, buf, x, y, w, h);
    }

    byte[] b = delegate.openBytes(no / getSizeC(), x, y, w, h);
    int bpp = FormatTools.getBytesPerPixel(getPixelType());
    int c = getZCTCoords(no)[1];
    ImageTools.splitChannels(b, buf, c, getSizeC(), bpp, false, isInterleaved(), w * h * bpp);
    return buf;
  }
  /* @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
    }
  }
Esempio n. 5
0
 @SuppressWarnings({"rawtypes", "unchecked"})
 private void populatePlane(IFormatReader r, int no, byte[] plane, PlanarAccess planarAccess) {
   final int pixelType = r.getPixelType();
   final int bpp = FormatTools.getBytesPerPixel(pixelType);
   final boolean fp = FormatTools.isFloatingPoint(pixelType);
   final boolean little = r.isLittleEndian();
   Object planeArray = DataTools.makeDataArray(plane, bpp, fp, little);
   if (planeArray == plane) {
     // array was returned by reference; make a copy
     final byte[] planeCopy = new byte[plane.length];
     System.arraycopy(plane, 0, planeCopy, 0, plane.length);
     planeArray = planeCopy;
   }
   planarAccess.setPlane(no, makeArray(planeArray));
 }
  /* @see loci.formats.IFormatHandler#openThumbBytes(int) */
  public byte[] openThumbBytes(int no) throws FormatException, IOException {
    FormatTools.assertId(currentId, true, 1);

    int currentSeries = getSeries();
    int thumbSize =
        getThumbSizeX()
            * getThumbSizeY()
            * FormatTools.getBytesPerPixel(getPixelType())
            * getRGBChannelCount();

    if (getCoreIndex() >= usedFiles.length - 1 || usedFiles.length >= core.length) {
      return super.openThumbBytes(no);
    }

    setSeries(usedFiles.length);
    byte[] thumb = FormatTools.openThumbBytes(this, 0);
    setSeries(currentSeries);
    if (thumb.length == thumbSize) {
      return thumb;
    }
    return super.openThumbBytes(no);
  }
Esempio n. 7
0
 @BeforeMethod
 public void setUp() throws Exception {
   fullPlaneCallIndex = 1;
   // No mapping.
   // Location.mapId(TEST_FILE, TEST_FILE);
   reader = new FakeReader();
   try {
     String uuid = UUID.randomUUID().toString();
     idDir = new File(System.getProperty("java.io.tmpdir"), uuid);
     idDir.mkdirs();
     File tempFile = new File(idDir, TEST_FILE);
     tempFile.createNewFile();
     id = tempFile.getAbsolutePath();
     reader.setId(id);
     sizeX = reader.getSizeX();
     sizeY = reader.getSizeY();
     bpp = FormatTools.getBytesPerPixel(reader.getPixelType());
     planeSize = sizeY * sizeY * bpp;
   } finally {
     reader.close();
   }
   reader = new FakeReader(); // No setId !
 }
  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;
  }
 public static int getBytesPerPixel() {
   return FormatTools.getBytesPerPixel(reader.getPixelType());
 }
Esempio n. 10
0
 private int getTileSize() {
   int channels = getRGBChannelCount();
   int bpp = FormatTools.getBytesPerPixel(getPixelType());
   return bpp * channels * tileX[getCoreIndex()] * tileY[getCoreIndex()];
 }
Esempio n. 11
0
  /* @see loci.formats.FormatReader#initFile(String) */
  public void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    MetadataLevel level = getMetadataOptions().getMetadataLevel();

    LOGGER.info("Reading header");

    // check endianness

    in.seek(ENDIANNESS_OFFSET);
    core[0].littleEndian = in.read() == 68;

    // read dimension information from 1024 byte header

    in.seek(0);
    in.order(isLittleEndian());

    core[0].sizeX = in.readInt();
    core[0].sizeY = in.readInt();
    core[0].sizeZ = in.readInt();

    // We are using BigInteger here because of the very real possiblity
    // of not just an int overflow but also a long overflow when multiplying
    // sizeX * sizeY * sizeZ.
    BigInteger v = BigInteger.valueOf(getSizeX());
    v = v.multiply(BigInteger.valueOf(getSizeY()));
    v = v.multiply(BigInteger.valueOf(getSizeZ()));
    if (getSizeX() < 0
        || getSizeY() < 0
        || getSizeZ() < 0
        || (v.compareTo(BigInteger.valueOf(in.length())) > 0)) {
      LOGGER.debug("Detected endianness is wrong, swapping");
      core[0].littleEndian = !isLittleEndian();
      in.seek(0);
      in.order(isLittleEndian());
      core[0].sizeX = in.readInt();
      core[0].sizeY = in.readInt();
      core[0].sizeZ = in.readInt();
    }

    core[0].sizeC = 1;

    int mode = in.readInt();
    switch (mode) {
      case 0:
        core[0].pixelType = FormatTools.UINT8;
        break;
      case 1:
        core[0].pixelType = FormatTools.INT16;
        break;
      case 6:
        core[0].pixelType = FormatTools.UINT16;
        break;
      case 2:
        core[0].pixelType = FormatTools.FLOAT;
        break;
      case 3:
        core[0].pixelType = FormatTools.UINT32;
        break;
      case 4:
        core[0].pixelType = FormatTools.DOUBLE;
        break;
      case 16:
        core[0].sizeC = 3;
        core[0].pixelType = FormatTools.UINT16;
        break;
    }

    in.skipBytes(12);

    // pixel size = xlen / mx

    double xSize = 0d, ySize = 0d, zSize = 0d;

    if (level != MetadataLevel.MINIMUM) {
      int mx = in.readInt();
      int my = in.readInt();
      int mz = in.readInt();

      // physical sizes are stored in ångströms, we want them in µm
      xSize = (in.readFloat() / mx) / 10000.0;
      ySize = (in.readFloat() / my) / 10000.0;
      zSize = (in.readFloat() / mz) / 10000.0;

      addGlobalMeta("Pixel size (X)", xSize);
      addGlobalMeta("Pixel size (Y)", ySize);
      addGlobalMeta("Pixel size (Z)", zSize);

      addGlobalMeta("Alpha angle", in.readFloat());
      addGlobalMeta("Beta angle", in.readFloat());
      addGlobalMeta("Gamma angle", in.readFloat());

      in.skipBytes(12);

      // min, max and mean pixel values
    } else in.skipBytes(48);

    double minValue = in.readFloat();
    double maxValue = in.readFloat();

    addGlobalMeta("Minimum pixel value", minValue);
    addGlobalMeta("Maximum pixel value", maxValue);
    addGlobalMeta("Mean pixel value", in.readFloat());

    int bytes = FormatTools.getBytesPerPixel(getPixelType());
    double range = Math.pow(2, bytes * 8) - 1;
    double pixelTypeMin = 0;
    boolean signed = FormatTools.isSigned(getPixelType());
    if (signed) {
      pixelTypeMin -= (range / 2);
    }
    double pixelTypeMax = pixelTypeMin + range;

    if (pixelTypeMax < maxValue || pixelTypeMin > minValue && signed) {
      // make the pixel type unsigned
      switch (getPixelType()) {
        case FormatTools.INT8:
          core[0].pixelType = FormatTools.UINT8;
          break;
        case FormatTools.INT16:
          core[0].pixelType = FormatTools.UINT16;
          break;
        case FormatTools.INT32:
          core[0].pixelType = FormatTools.UINT32;
          break;
      }
    }

    in.skipBytes(4);

    extHeaderSize = in.readInt();

    if (level != MetadataLevel.MINIMUM) {
      in.skipBytes(64);

      int idtype = in.readShort();

      String type = "unknown";
      if (idtype >= 0 && idtype < TYPES.length) type = TYPES[idtype];

      addGlobalMeta("Series type", type);
      addGlobalMeta("Lens", in.readShort());
      addGlobalMeta("ND1", in.readShort());
      addGlobalMeta("ND2", in.readShort());
      addGlobalMeta("VD1", in.readShort());
      addGlobalMeta("VD2", in.readShort());

      for (int i = 0; i < 6; i++) {
        addGlobalMeta("Angle " + (i + 1), in.readFloat());
      }

      in.skipBytes(24);

      addGlobalMeta("Number of useful labels", in.readInt());

      for (int i = 0; i < 10; i++) {
        addGlobalMeta("Label " + (i + 1), in.readString(80));
      }
    }

    LOGGER.info("Populating metadata");

    core[0].sizeT = 1;
    core[0].dimensionOrder = "XYZTC";
    core[0].imageCount = getSizeZ();
    core[0].rgb = false;
    core[0].interleaved = true;
    core[0].indexed = false;
    core[0].falseColor = false;
    core[0].metadataComplete = true;

    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);

    if (level != MetadataLevel.MINIMUM) {
      if (xSize - Constants.EPSILON > 0) {
        store.setPixelsPhysicalSizeX(new PositiveFloat(xSize), 0);
      } else {
        LOGGER.warn("xSize {} not a positive float skipping", xSize);
      }
      if (ySize - Constants.EPSILON > 0) {
        store.setPixelsPhysicalSizeY(new PositiveFloat(ySize), 0);
      } else {
        LOGGER.warn("ySize {} not a positive float skipping", ySize);
      }
      if (zSize - Constants.EPSILON > 0) {
        store.setPixelsPhysicalSizeZ(new PositiveFloat(zSize), 0);
      } else {
        LOGGER.warn("zSize {} not a positive float skipping", zSize);
      }
    }
  }
Esempio n. 12
0
  /** @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int) */
  public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
      throws FormatException, IOException {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);

    int index = no;
    for (int i = 0; i < series; i++) {
      index += core[i].imageCount;
    }
    if (index >= binDataOffsets.size()) {
      index = binDataOffsets.size() - 1;
    }

    long offset = binDataOffsets.get(index).longValue();
    String compress = compression.get(index);

    in.seek(offset);

    int depth = FormatTools.getBytesPerPixel(getPixelType());
    int planeSize = getSizeX() * getSizeY() * depth;

    CodecOptions options = new CodecOptions();
    options.width = getSizeX();
    options.height = getSizeY();
    options.bitsPerSample = depth * 8;
    options.channels = getRGBChannelCount();
    options.maxBytes = planeSize;
    options.littleEndian = isLittleEndian();
    options.interleaved = isInterleaved();

    byte[] pixels = new Base64Codec().decompress(in, options);

    // return a blank plane if no pixel data was stored
    if (pixels.length == 0) {
      LOGGER.debug("No pixel data for plane #{}", no);
      return buf;
    }

    // TODO: Create a method uncompress to handle all compression methods
    if (compress.equals("bzip2")) {
      byte[] tempPixels = pixels;
      pixels = new byte[tempPixels.length - 2];
      System.arraycopy(tempPixels, 2, pixels, 0, pixels.length);

      ByteArrayInputStream bais = new ByteArrayInputStream(pixels);
      CBZip2InputStream bzip = new CBZip2InputStream(bais);
      pixels = new byte[planeSize];
      bzip.read(pixels, 0, pixels.length);
      tempPixels = null;
      bais.close();
      bais = null;
      bzip = null;
    } else if (compress.equals("zlib")) {
      pixels = new ZlibCodec().decompress(pixels, options);
    } else if (compress.equals("J2K")) {
      pixels = new JPEG2000Codec().decompress(pixels, options);
    } else if (compress.equals("JPEG")) {
      pixels = new JPEGCodec().decompress(pixels, options);
    }

    for (int row = 0; row < h; row++) {
      int off = (row + y) * getSizeX() * depth + x * depth;
      System.arraycopy(pixels, off, buf, row * w * depth, w * depth);
    }

    pixels = null;

    return buf;
  }