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

Example 51 with MetadataRetrieve

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

the class LegacyQTWriter 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);
}

Example 52 with MetadataRetrieve

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

the class OMEXMLWriter method setId.

// -- FormatWriter API methods --
/* @see loci.formats.FormatWriter#setId(String) */
@Override
public void setId(String id) throws FormatException, IOException {
    if (id.equals(currentId)) {
        return;
    }
    super.setId(id);
    MetadataRetrieve retrieve = getMetadataRetrieve();
    String xml;
    try {
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(OMEXMLService.class);
        xml = service.getOMEXML(retrieve);
        OMEXMLMetadata noBin = service.createOMEXMLMetadata(xml);
        service.removeBinData(noBin);
        OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) noBin.getRoot();
        root.setCreator(FormatTools.CREATOR);
        xml = service.getOMEXML(noBin);
    } catch (DependencyException de) {
        throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
    } catch (ServiceException se) {
        throw new FormatException(se);
    }
    xmlFragments = new ArrayList<String>();
    currentFragment = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
    XMLTools.parseXML(xml, new OMEHandler());
    xmlFragments.add(currentFragment);
}

Example 53 with MetadataRetrieve

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

the class OMEXMLWriter method close.

/* @see loci.formats.IFormatHandler#close() */
@Override
public void close() throws IOException {
    if (out != null) {
        out.writeBytes(xmlFragments.get(xmlFragments.size() - 1));
    }
    if (getMetadataOptions().isValidate()) {
        try {
            MetadataRetrieve r = getMetadataRetrieve();
            String omexml = service.getOMEXML(r);
            service.validateOMEXML(omexml);
        } catch (ServiceException | NullPointerException e) {
            LOGGER.warn("OMEXMLService unable to create OME-XML metadata object.", e);
        }
    }
    super.close();
    xmlFragments = null;
    service = null;
}

Example 54 with MetadataRetrieve

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

the class ICSWriter 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 (pixels == null) {
        pixels = new RandomAccessOutputStream(currentId);
    }
    MetadataRetrieve meta = getMetadataRetrieve();
    int rgbChannels = getSamplesPerPixel();
    String order = meta.getPixelsDimensionOrder(series).getValue();
    int sizeZ = meta.getPixelsSizeZ(series).getValue().intValue();
    int sizeC = meta.getChannelCount(series);
    if (rgbChannels <= sizeC) {
        sizeC /= rgbChannels;
    }
    int sizeT = meta.getPixelsSizeT(series).getValue().intValue();
    int planes = sizeZ * sizeC * sizeT;
    int[] coords = FormatTools.getZCTCoords(order, sizeZ, sizeC, sizeT, planes, no);
    int realIndex = FormatTools.getIndex(outputOrder, sizeZ, sizeC, sizeT, planes, coords[0], coords[1], coords[2]);
    if (uniqueFiles.size() > 1) {
        realIndex = no;
    }
    int sizeX = meta.getPixelsSizeX(series).getValue().intValue();
    int sizeY = meta.getPixelsSizeY(series).getValue().intValue();
    int pixelType = FormatTools.pixelTypeFromString(meta.getPixelsType(series).toString());
    int bytesPerPixel = FormatTools.getBytesPerPixel(pixelType);
    long planeSize = sizeX * sizeY * rgbChannels * bytesPerPixel;
    if (!initialized[series][realIndex]) {
        initialized[series][realIndex] = true;
        if (!isFullPlane(x, y, w, h)) {
            // write a dummy plane that will be overwritten in sections
            pixels.seek(pixelOffset + (realIndex + 1) * planeSize);
        }
    }
    pixels.seek(pixelOffset + realIndex * planeSize);
    if (isFullPlane(x, y, w, h) && (interleaved || rgbChannels == 1)) {
        pixels.write(buf);
    } else {
        pixels.skipBytes(bytesPerPixel * rgbChannels * sizeX * y);
        for (int row = 0; row < h; row++) {
            ByteArrayOutputStream strip = new ByteArrayOutputStream();
            for (int col = 0; col < w; col++) {
                for (int c = 0; c < rgbChannels; c++) {
                    int index = interleaved ? rgbChannels * (row * w + col) + c : w * (c * h + row) + col;
                    strip.write(buf, index * bytesPerPixel, bytesPerPixel);
                }
            }
            pixels.skipBytes(bytesPerPixel * rgbChannels * x);
            pixels.write(strip.toByteArray());
            pixels.skipBytes(bytesPerPixel * rgbChannels * (sizeX - w - x));
        }
    }
    lastPlane = realIndex;
    overwriteDimensions(getMetadataRetrieve());
    pixels.close();
    pixels = null;
}

Example 55 with MetadataRetrieve

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

the class JPEG2000Writer method compressBuffer.

/**
 * Compresses the buffer.
 *
 * @param no the image index within the current file, starting from 0.
 * @param buf the byte array that represents the image tile.
 * @param x the X coordinate of the upper-left corner of the image tile.
 * @param y the Y coordinate of the upper-left corner of the image tile.
 * @param w the width (in pixels) of the image tile.
 * @param h the height (in pixels) of the image tile.
 * @throws FormatException if one of the parameters is invalid.
 * @throws IOException if there was a problem writing to the file.
 */
public byte[] compressBuffer(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    checkParams(no, buf, x, y, w, h);
    MetadataRetrieve retrieve = getMetadataRetrieve();
    boolean littleEndian = false;
    if (retrieve.getPixelsBigEndian(series) != null) {
        littleEndian = !retrieve.getPixelsBigEndian(series).booleanValue();
    } else if (retrieve.getPixelsBinDataCount(series) == 0) {
        littleEndian = !retrieve.getPixelsBinDataBigEndian(series, 0).booleanValue();
    }
    int bytesPerPixel = FormatTools.getBytesPerPixel(FormatTools.pixelTypeFromString(retrieve.getPixelsType(series).toString()));
    int nChannels = getSamplesPerPixel();
    // To be on the save-side
    if (options == null)
        options = JPEG2000CodecOptions.getDefaultOptions();
    options = new JPEG2000CodecOptions(options);
    options.width = w;
    options.height = h;
    options.channels = nChannels;
    options.bitsPerSample = bytesPerPixel * 8;
    options.littleEndian = littleEndian;
    options.interleaved = interleaved;
    options.lossless = compression == null || compression.equals(CompressionType.J2K.getCompression());
    options.colorModel = getColorModel();
    return new JPEG2000Codec().compress(buf, options);
}