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

Example 56 with MetadataRetrieve

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

the class JavaWriter 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("JavaWriter does not yet support saving image tiles.");
    }
    // check pixel type
    MetadataRetrieve meta = getMetadataRetrieve();
    String pixelType = meta.getPixelsType(series).toString();
    int type = FormatTools.pixelTypeFromString(pixelType);
    if (!DataTools.containsValue(getPixelTypes(), type)) {
        throw new FormatException("Unsupported image type '" + pixelType + "'.");
    }
    int bpp = FormatTools.getBytesPerPixel(type);
    boolean fp = FormatTools.isFloatingPoint(type);
    boolean little = false;
    if (meta.getPixelsBigEndian(series) != null) {
        little = !meta.getPixelsBigEndian(series).booleanValue();
    } else if (meta.getPixelsBinDataCount(series) == 0) {
        little = !meta.getPixelsBinDataBigEndian(series, 0).booleanValue();
    }
    // write array
    String varName = "series" + series + "Plane" + no;
    Object array = DataTools.makeDataArray(buf, bpp, fp, little);
    out.seek(out.length());
    if (array instanceof byte[]) {
        writePlane(varName, (byte[]) array, w, h);
    } else if (array instanceof short[]) {
        writePlane(varName, (short[]) array, w, h);
    } else if (array instanceof int[]) {
        writePlane(varName, (int[]) array, w, h);
    } else if (array instanceof long[]) {
        writePlane(varName, (long[]) array, w, h);
    } else if (array instanceof float[]) {
        writePlane(varName, (float[]) array, w, h);
    } else if (array instanceof double[]) {
        writePlane(varName, (double[]) array, w, h);
    }
}

Example 57 with MetadataRetrieve

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

the class OMETiffWriter method setupServiceAndMetadata.

private void setupServiceAndMetadata() throws DependencyException, ServiceException {
    // extract OME-XML string from metadata object
    MetadataRetrieve retrieve = getMetadataRetrieve();
    ServiceFactory factory = new ServiceFactory();
    service = factory.getInstance(OMEXMLService.class);
    OMEXMLMetadata originalOMEMeta = service.getOMEMetadata(retrieve);
    originalOMEMeta.resolveReferences();
    String omexml = service.getOMEXML(originalOMEMeta);
    omeMeta = service.createOMEXMLMetadata(omexml);
}

Example 58 with MetadataRetrieve

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

the class QTWriter method setId.

// -- FormatWriter API methods --
/* @see loci.formats.FormatWriter#setId(String) */
@Override
public void setId(String id) throws FormatException, IOException {
    super.setId(id);
    MetadataRetrieve r = getMetadataRetrieve();
    MetadataTools.verifyMinimumPopulated(r, series);
    int width = r.getPixelsSizeX(series).getValue().intValue();
    int height = r.getPixelsSizeY(series).getValue().intValue();
    int nChannels = getSamplesPerPixel();
    int planeSize = width * height * nChannels;
    pad = nChannels > 1 ? 0 : (4 - (width % 4)) % 4;
    if (legacy == null) {
        legacy = new LegacyQTWriter();
        legacy.setCodec(codec);
        legacy.setMetadataRetrieve(r);
    }
    offsets = new ArrayList<Integer>();
    created = (int) System.currentTimeMillis();
    numBytes = 0;
    if (out.length() == 0) {
        // -- write the first header --
        writeAtom(8, "wide");
        writeAtom(numBytes + 8, "mdat");
        numWritten = 0;
    } else {
        out.seek(BYTE_COUNT_OFFSET);
        RandomAccessInputStream in = new RandomAccessInputStream(currentId);
        in.seek(BYTE_COUNT_OFFSET);
        numBytes = in.readInt() - 8;
        numWritten = numBytes / (planeSize + pad * height);
        in.close();
    }
    for (int i = 0; i < getPlaneCount(); i++) {
        offsets.add(16 + i * (planeSize + pad * height));
    }
}

Example 59 with MetadataRetrieve

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

the class QTWriter method writeFooter.

private void writeFooter() throws IOException {
    out.seek(out.length());
    MetadataRetrieve r = getMetadataRetrieve();
    int width = r.getPixelsSizeX(series).getValue().intValue();
    int height = r.getPixelsSizeY(series).getValue().intValue();
    int nChannels = getSamplesPerPixel();
    int timeScale = 1000;
    int duration = (int) (numWritten * ((double) timeScale / fps));
    int bitsPerPixel = (nChannels > 1) ? 24 : 40;
    int channels = (bitsPerPixel >= 40) ? 1 : 3;
    // -- write moov atom --
    int atomLength = 685 + 8 * numWritten;
    writeAtom(atomLength, "moov");
    // -- write mvhd atom --
    writeAtom(108, "mvhd");
    // version
    out.writeShort(0);
    // flags
    out.writeShort(0);
    // creation time
    out.writeInt(created);
    out.writeInt((int) System.currentTimeMillis());
    // time scale
    out.writeInt(timeScale);
    // duration
    out.writeInt(duration);
    // preferred rate & volume
    out.write(new byte[] { 0, 1, 0, 0 });
    // reserved
    out.write(new byte[] { 0, -1, 0, 0, 0, 0, 0, 0, 0, 0 });
    writeRotationMatrix();
    // not sure what this is
    out.writeShort(0);
    // preview duration
    out.writeInt(0);
    // preview time
    out.writeInt(0);
    // poster time
    out.writeInt(0);
    // selection time
    out.writeInt(0);
    // selection duration
    out.writeInt(0);
    // current time
    out.writeInt(0);
    // next track's id
    out.writeInt(2);
    // -- write trak atom --
    atomLength -= 116;
    writeAtom(atomLength, "trak");
    // -- write tkhd atom --
    writeAtom(92, "tkhd");
    // version
    out.writeShort(0);
    // flags
    out.writeShort(15);
    // creation time
    out.writeInt(created);
    out.writeInt((int) System.currentTimeMillis());
    // track id
    out.writeInt(1);
    // reserved
    out.writeInt(0);
    // duration
    out.writeInt(duration);
    // reserved
    out.writeInt(0);
    // reserved
    out.writeInt(0);
    // reserved
    out.writeShort(0);
    // unknown
    out.writeInt(0);
    writeRotationMatrix();
    // image width
    out.writeInt(width);
    // image height
    out.writeInt(height);
    // reserved
    out.writeShort(0);
    // -- write edts atom --
    writeAtom(36, "edts");
    // -- write elst atom --
    writeAtom(28, "elst");
    // version
    out.writeShort(0);
    // flags
    out.writeShort(0);
    // number of entries in the table
    out.writeInt(1);
    // duration
    out.writeInt(duration);
    // time
    out.writeShort(0);
    // rate
    out.writeInt(1);
    // unknown
    out.writeShort(0);
    // -- write mdia atom --
    atomLength -= 136;
    writeAtom(atomLength, "mdia");
    // -- write mdhd atom --
    writeAtom(32, "mdhd");
    // version
    out.writeShort(0);
    // flags
    out.writeShort(0);
    // creation time
    out.writeInt(created);
    out.writeInt((int) System.currentTimeMillis());
    // time scale
    out.writeInt(timeScale);
    // duration
    out.writeInt(duration);
    // language
    out.writeShort(0);
    // quality
    out.writeShort(0);
    // -- write hdlr atom --
    writeAtom(58, "hdlr");
    // version
    out.writeShort(0);
    // flags
    out.writeShort(0);
    out.writeBytes("mhlr");
    out.writeBytes("vide");
    out.writeBytes("appl");
    out.write(new byte[] { 16, 0, 0, 0, 0, 1, 1, 11, 25 });
    out.writeBytes("Apple Video Media Handler");
    // -- write minf atom --
    atomLength -= 98;
    writeAtom(atomLength, "minf");
    // -- write vmhd atom --
    writeAtom(20, "vmhd");
    // version
    out.writeShort(0);
    // flags
    out.writeShort(1);
    // graphics mode
    out.writeShort(64);
    // opcolor 1
    out.writeShort(32768);
    // opcolor 2
    out.writeShort(32768);
    // opcolor 3
    out.writeShort(32768);
    // -- write hdlr atom --
    writeAtom(57, "hdlr");
    // version
    out.writeShort(0);
    // flags
    out.writeShort(0);
    out.writeBytes("dhlr");
    out.writeBytes("alis");
    out.writeBytes("appl");
    out.write(new byte[] { 16, 0, 0, 1, 0, 1, 1, 31, 24 });
    out.writeBytes("Apple Alias Data Handler");
    // -- write dinf atom --
    writeAtom(36, "dinf");
    // -- write dref atom --
    writeAtom(28, "dref");
    // version
    out.writeShort(0);
    // flags
    out.writeShort(0);
    // version 2
    out.writeShort(0);
    // flags 2
    out.writeShort(1);
    out.write(new byte[] { 0, 0, 0, 12 });
    out.writeBytes("alis");
    // version 3
    out.writeShort(0);
    // flags 3
    out.writeShort(1);
    // -- write stbl atom --
    atomLength -= 121;
    writeAtom(atomLength, "stbl");
    // -- write stsd atom --
    writeAtom(118, "stsd");
    // version
    out.writeShort(0);
    // flags
    out.writeShort(0);
    // number of entries in the table
    out.writeInt(1);
    out.write(new byte[] { 0, 0, 0, 102 });
    // codec
    out.writeBytes("raw ");
    // reserved
    out.write(new byte[] { 0, 0, 0, 0, 0, 0 });
    // data reference
    out.writeShort(1);
    // version
    out.writeShort(1);
    // revision
    out.writeShort(1);
    out.writeBytes("appl");
    // temporal quality
    out.writeInt(0);
    // spatial quality
    out.writeInt(768);
    // image width
    out.writeShort(width);
    // image height
    out.writeShort(height);
    byte[] dpi = new byte[] { 0, 72, 0, 0 };
    // horizontal dpi
    out.write(dpi);
    // vertical dpi
    out.write(dpi);
    // data size
    out.writeInt(0);
    // frames per sample
    out.writeShort(1);
    // length of compressor name
    out.writeShort(12);
    // compressor name
    out.writeBytes("Uncompressed");
    // unknown
    out.writeInt(bitsPerPixel);
    // unknown
    out.writeInt(bitsPerPixel);
    // unknown
    out.writeInt(bitsPerPixel);
    // unknown
    out.writeInt(bitsPerPixel);
    // unknown
    out.writeInt(bitsPerPixel);
    // bits per pixel
    out.writeShort(bitsPerPixel);
    // ctab ID
    out.writeInt(65535);
    // gamma
    out.write(new byte[] { 12, 103, 97, 108 });
    // unknown
    out.write(new byte[] { 97, 1, -52, -52, 0, 0, 0, 0 });
    // -- write stts atom --
    writeAtom(24, "stts");
    // version
    out.writeShort(0);
    // flags
    out.writeShort(0);
    // number of entries in the table
    out.writeInt(1);
    // number of planes
    out.writeInt(numWritten);
    // milliseconds per frame
    out.writeInt((int) ((double) timeScale / fps));
    // -- write stsc atom --
    writeAtom(28, "stsc");
    // version
    out.writeShort(0);
    // flags
    out.writeShort(0);
    // number of entries in the table
    out.writeInt(1);
    // chunk
    out.writeInt(1);
    // samples
    out.writeInt(1);
    // id
    out.writeInt(1);
    // -- write stsz atom --
    writeAtom(20 + 4 * numWritten, "stsz");
    // version
    out.writeShort(0);
    // flags
    out.writeShort(0);
    // sample size
    out.writeInt(0);
    // number of planes
    out.writeInt(numWritten);
    for (int i = 0; i < numWritten; i++) {
        // sample size
        out.writeInt(channels * height * (width + pad));
    }
    // -- write stco atom --
    writeAtom(16 + 4 * numWritten, "stco");
    // version
    out.writeShort(0);
    // flags
    out.writeShort(0);
    // number of planes
    out.writeInt(numWritten);
    for (int i = 0; i < numWritten; i++) {
        // write the plane offset
        out.writeInt(offsets.get(i));
    }
}

Example 60 with MetadataRetrieve

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

the class TiffWriter method saveBytes.

/**
 * Saves the given image to the specified series in the current file.
 * The IFD hashtable allows specification of TIFF parameters such as bit
 * depth, compression and units.
 */
public void saveBytes(int no, byte[] buf, IFD ifd, int x, int y, int w, int h) throws IOException, FormatException {
    if (checkParams)
        checkParams(no, buf, x, y, w, h);
    if (ifd == null)
        ifd = new IFD();
    MetadataRetrieve retrieve = getMetadataRetrieve();
    int type = FormatTools.pixelTypeFromString(retrieve.getPixelsType(series).toString());
    int index = no;
    int imageWidth = retrieve.getPixelsSizeX(series).getValue().intValue();
    int imageHeight = retrieve.getPixelsSizeY(series).getValue().intValue();
    int currentTileSizeX = getTileSizeX();
    int currentTileSizeY = getTileSizeY();
    if (currentTileSizeX != imageWidth || currentTileSizeY != imageHeight) {
        ifd.put(new Integer(IFD.TILE_WIDTH), new Long(currentTileSizeX));
        ifd.put(new Integer(IFD.TILE_LENGTH), new Long(currentTileSizeY));
    }
    if (currentTileSizeX < w || currentTileSizeY < h) {
        int numTilesX = (w + (x % currentTileSizeX) + currentTileSizeX - 1) / currentTileSizeX;
        int numTilesY = (h + (y % currentTileSizeY) + currentTileSizeY - 1) / currentTileSizeY;
        for (int yTileIndex = 0; yTileIndex < numTilesY; yTileIndex++) {
            for (int xTileIndex = 0; xTileIndex < numTilesX; xTileIndex++) {
                Region tileParams = new Region();
                tileParams.width = xTileIndex < numTilesX - 1 ? currentTileSizeX - (x % currentTileSizeX) : w - (currentTileSizeX * xTileIndex);
                tileParams.height = yTileIndex < numTilesY - 1 ? currentTileSizeY - (y % currentTileSizeY) : h - (currentTileSizeY * yTileIndex);
                tileParams.x = x + (xTileIndex * currentTileSizeX) - (xTileIndex > 0 ? (x % currentTileSizeX) : 0);
                tileParams.y = y + (yTileIndex * currentTileSizeY) - (yTileIndex > 0 ? (y % currentTileSizeY) : 0);
                byte[] tileBuf = getTile(buf, tileParams, new Region(x, y, w, h));
                // This operation is synchronized
                synchronized (this) {
                    // This operation is synchronized against the TIFF saver.
                    synchronized (tiffSaver) {
                        index = prepareToWriteImage(no, tileBuf, ifd, tileParams.x, tileParams.y, tileParams.width, tileParams.height);
                        if (index == -1) {
                            return;
                        }
                    }
                }
                tiffSaver.writeImage(tileBuf, ifd, index, type, tileParams.x, tileParams.y, tileParams.width, tileParams.height, no == getPlaneCount() - 1 && getSeries() == retrieve.getImageCount() - 1);
            }
        }
    } else {
        // This operation is synchronized
        synchronized (this) {
            // This operation is synchronized against the TIFF saver.
            synchronized (tiffSaver) {
                index = prepareToWriteImage(no, buf, ifd, x, y, w, h);
                if (index == -1) {
                    return;
                }
            }
        }
        tiffSaver.writeImage(buf, ifd, index, type, x, y, w, h, no == getPlaneCount() - 1 && getSeries() == retrieve.getImageCount() - 1);
    }
}