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

Example 16 with MetadataRetrieve

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

the class FormatWriter method getSamplesPerPixel.

/**
 * Retrieve the number of samples per pixel for given series.
 */
protected int getSamplesPerPixel(int series) {
    MetadataRetrieve r = getMetadataRetrieve();
    PositiveInteger samples = r.getChannelSamplesPerPixel(series, 0);
    if (samples == null) {
        LOGGER.warn("SamplesPerPixel #0 is null. It is assumed to be 1.");
    }
    return samples == null ? 1 : samples.getValue();
}

Example 17 with MetadataRetrieve

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

the class OrthogonalReader method initialiseWriter.

private OMETiffWriter initialiseWriter(String fileName, ImageReader reader) throws Exception {
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata metadata = service.createOMEXMLMetadata();
    MetadataRetrieve mr = (MetadataRetrieve) reader.getMetadataStore();
    Length originalSizeX = mr.getPixelsPhysicalSizeX(0);
    Length originalSizeY = mr.getPixelsPhysicalSizeY(0);
    Length originalSizeZ = mr.getPixelsPhysicalSizeZ(0);
    // Original XY planes
    // XZ planes
    MetadataTools.populateMetadata(metadata, 0, "XZ", reader.isLittleEndian(), reader.getDimensionOrder(), FormatTools.getPixelTypeString(reader.getPixelType()), reader.getSizeX(), reader.getSizeZ(), reader.getSizeY(), 1, 1, 1);
    metadata.setPixelsPhysicalSizeX(originalSizeX, 0);
    metadata.setPixelsPhysicalSizeY(originalSizeZ, 0);
    metadata.setPixelsPhysicalSizeZ(originalSizeY, 0);
    // YZ planes
    MetadataTools.populateMetadata(metadata, 1, "YZ", reader.isLittleEndian(), reader.getDimensionOrder(), FormatTools.getPixelTypeString(reader.getPixelType()), reader.getSizeY(), reader.getSizeZ(), reader.getSizeX(), 1, 1, 1);
    metadata.setPixelsPhysicalSizeX(originalSizeY, 1);
    metadata.setPixelsPhysicalSizeY(originalSizeZ, 1);
    metadata.setPixelsPhysicalSizeZ(originalSizeX, 1);
    OMETiffWriter writer = new OMETiffWriter();
    writer.setMetadataRetrieve(metadata);
    writer.setId(fileName);
    return writer;
}

Example 18 with MetadataRetrieve

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

the class APNGWriter method setId.

// -- FormatWriter API methods --
/* @see loci.formats.FormatWriter#setId(String) */
@Override
public void setId(String id) throws FormatException, IOException {
    super.setId(id);
    if (out.length() == 0) {
        numFrames = 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);
        if (r.getPixelsBigEndian(series) != null) {
            littleEndian = !r.getPixelsBigEndian(series).booleanValue();
        } else if (r.getPixelsBinDataCount(series) == 0) {
            littleEndian = !r.getPixelsBinDataBigEndian(series, 0).booleanValue();
        }
        // 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);
        // save a place for the CRC
        out.writeInt(0);
        footerPointer = out.getFilePointer();
    } else {
        numFramesPointer = PNG_SIG.length + 33;
        RandomAccessInputStream in = new RandomAccessInputStream(id);
        in.order(littleEndian);
        in.seek(8);
        while (in.getFilePointer() < in.length()) {
            int length = in.readInt();
            String type = in.readString(4);
            if (type.equals("fcTL") || type.equals("fdAT")) {
                nextSequenceNumber = in.readInt() + 1;
                length -= 4;
            }
            in.skipBytes(length + 4);
        }
        in.seek(numFramesPointer);
        numFrames = in.readInt();
        in.close();
        footerPointer = out.length() - 12;
    }
    if (numFrames == 0) {
        nextSequenceNumber = 0;
    }
}

Example 19 with MetadataRetrieve

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

the class EPSWriter method writeHeader.

// -- Helper methods --
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: " + FormatTools.CREATOR + "\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();
}

Example 20 with MetadataRetrieve

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

the class OMEXMLWriter method compress.

// -- Helper methods --
/**
 * Compress the given byte array using the current codec.
 * The compressed data is then base64-encoded.
 */
private byte[] compress(byte[] b) throws FormatException, IOException {
    MetadataRetrieve r = getMetadataRetrieve();
    String type = r.getPixelsType(series).toString();
    int pixelType = FormatTools.pixelTypeFromString(type);
    int bytes = FormatTools.getBytesPerPixel(pixelType);
    CodecOptions options = new CodecOptions();
    options.width = r.getPixelsSizeX(series).getValue().intValue();
    options.height = r.getPixelsSizeY(series).getValue().intValue();
    options.channels = 1;
    options.interleaved = false;
    options.signed = FormatTools.isSigned(pixelType);
    boolean littleEndian = false;
    if (r.getPixelsBigEndian(series) != null) {
        littleEndian = !r.getPixelsBigEndian(series).booleanValue();
    } else if (r.getPixelsBinDataCount(series) == 0) {
        littleEndian = !r.getPixelsBinDataBigEndian(series, 0).booleanValue();
    }
    options.littleEndian = littleEndian;
    options.bitsPerSample = bytes * 8;
    if (compression.equals("J2K")) {
        b = new JPEG2000Codec().compress(b, options);
    } else if (compression.equals("JPEG")) {
        b = new JPEGCodec().compress(b, options);
    } else if (compression.equals("zlib")) {
        b = new ZlibCodec().compress(b, options);
    }
    return new Base64Codec().compress(b, options);
}