Examples with MetadataRetrieve loci.formats.meta.MetadataRetrieve used on opensource projects

Example 46 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class LociFunctions method getSeriesName.

public void getSeriesName(String[] seriesName) {
    MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore();
    seriesName[0] = retrieve.getImageName(r.getSeries());
}

Example 47 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class APNGWriter method saveBytes.

// -- IFormatWriter API methods --
/**
 * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
 */
@Override
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();
    out.seek(footerPointer);
    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++;
    writeFooter();
}

Example 48 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class APNGWriter method writePixels.

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(Constants.ENCODING));
    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));
}

Example 49 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class EPSWriter method saveBytes.

// -- IFormatWriter API methods --
/**
 * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
 */
@Override
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();
    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;
    final StringBuilder buffer = new StringBuilder();
    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");
}

Example 50 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class ImageIOWriter method saveBytes.

// -- IFormatWriter API methods --
/**
 * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
 */
@Override
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();
    BufferedImage image = AWTImageTools.makeImage(buf, interleaved, meta, series);
    savePlane(no, image, x, y, w, h);
}