Examples with DeflaterOutputStream java.util.zip.DeflaterOutputStream used on opensource projects

Example 31 with DeflaterOutputStream

use of java.util.zip.DeflaterOutputStream in project vcell by virtualcell.

the class MicroscopyXmlproducer method getXML.

/**
 * This methods returns a XML represnetation of a VCImage object.
 * Creation date: (3/1/2001 3:02:37 PM)
 * @param param cbit.image.VCImage
 * @return Element
 * @throws XmlParseException
 */
private static Element getXML(UShortImage param, Xmlproducer vcellXMLProducer, boolean bSaveCompressed) throws XmlParseException {
    Element image = new Element(MicroscopyXMLTags.UShortImageTag);
    // add atributes
    if (param.getName() != null && param.getName().length() > 0) {
        image.setAttribute(XMLTags.NameAttrTag, mangle(param.getName()));
    }
    // Add annotation
    if (param.getDescription() != null && param.getDescription().length() > 0) {
        Element annotationElement = new Element(XMLTags.AnnotationTag);
        annotationElement.setText(mangle(param.getDescription()));
        image.addContent(annotationElement);
    }
    // Add extent
    if (param.getExtent() != null) {
        image.addContent(vcellXMLProducer.getXML(param.getExtent()));
    }
    // Add Origin
    if (param.getOrigin() != null) {
        image.addContent(vcellXMLProducer.getXML(param.getOrigin()));
    }
    final int BYTES_PER_SHORT = 2;
    int aNumX = param.getNumX();
    int aNumY = param.getNumY();
    int aNumZ = param.getNumZ();
    // Add Imagedata subelement
    int UNCOMPRESSED_SIZE_BYTES = aNumX * aNumY * aNumZ * BYTES_PER_SHORT;
    short[] pixelsShort = param.getPixels();
    byte[] compressedPixels = null;
    boolean bForceUncompressed = false;
    while (true) {
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        OutputStream dos = bos;
        if (bSaveCompressed && !bForceUncompressed) {
            dos = new DeflaterOutputStream(bos);
        }
        ByteBuffer byteBuffer = ByteBuffer.allocate(UNCOMPRESSED_SIZE_BYTES);
        for (int i = 0; i < pixelsShort.length; i++) {
            byteBuffer.putShort(pixelsShort[i]);
        }
        try {
            dos.write(byteBuffer.array());
        } catch (IOException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("failed to create compressed pixel data");
        } finally {
            if (dos != null) {
                try {
                    dos.close();
                } catch (Exception e2) {
                    e2.printStackTrace();
                }
            }
        }
        compressedPixels = bos.toByteArray();
        if (!bSaveCompressed || bForceUncompressed) {
            if (UNCOMPRESSED_SIZE_BYTES != compressedPixels.length) {
                throw new XmlParseException("failed to create uncompressed pixel data");
            }
        } else if (!bForceUncompressed) {
            if (UNCOMPRESSED_SIZE_BYTES <= compressedPixels.length) {
                // Compression didn't compress
                // Save uncompressed so reader not confused
                bForceUncompressed = true;
                continue;
            }
        }
        break;
    }
    Element imagedata = new Element(XMLTags.ImageDataTag);
    // Get imagedata attributes
    imagedata.setAttribute(XMLTags.XAttrTag, String.valueOf(aNumX));
    imagedata.setAttribute(XMLTags.YAttrTag, String.valueOf(aNumY));
    imagedata.setAttribute(XMLTags.ZAttrTag, String.valueOf(aNumZ));
    imagedata.setAttribute(XMLTags.CompressedSizeTag, String.valueOf(compressedPixels.length));
    // Get imagedata content
    // encode
    imagedata.addContent(org.vcell.util.Hex.toString(compressedPixels));
    // Add imagedata to VCImage element
    image.addContent(imagedata);
    return image;
}

Example 32 with DeflaterOutputStream

use of java.util.zip.DeflaterOutputStream in project vcell by virtualcell.

the class VCImageUncompressed method getPixelsCompressed.

/**
 * This method was created in VisualAge.
 * @return byte[]
 */
public byte[] getPixelsCompressed() throws ImageException {
    try {
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        DeflaterOutputStream dos = new DeflaterOutputStream(bos);
        // DeflaterOutputStream dos = new DeflaterOutputStream(bos,new Deflater(5,false));
        dos.write(pixels, 0, pixels.length);
        dos.close();
        return bos.toByteArray();
    } catch (IOException e) {
        e.printStackTrace(System.out);
        throw new ImageException(e.getMessage());
    }
}

Example 33 with DeflaterOutputStream

use of java.util.zip.DeflaterOutputStream in project vcell by virtualcell.

the class ByteImage method getPixelsCompressed.

/**
 * This method was created in VisualAge.
 * @return byte[]
 */
public byte[] getPixelsCompressed() throws ImageException {
    try {
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        DeflaterOutputStream dos = new DeflaterOutputStream(bos);
        // DeflaterOutputStream dos = new DeflaterOutputStream(bos,new Deflater(5,false));
        dos.write(pixels, 0, pixels.length);
        dos.close();
        return bos.toByteArray();
    } catch (IOException e) {
        e.printStackTrace(System.out);
        throw new ImageException(e.getMessage());
    }
}

Example 34 with DeflaterOutputStream

use of java.util.zip.DeflaterOutputStream in project vcell by virtualcell.

the class BeanUtils method toCompressedSerialized.

public static byte[] toCompressedSerialized(Serializable cacheObj) throws java.io.IOException {
    byte[] bytes = toSerialized(cacheObj);
    long before = System.currentTimeMillis();
    byte[] objData = null;
    java.io.ByteArrayOutputStream bos = new java.io.ByteArrayOutputStream();
    DeflaterOutputStream dos = new DeflaterOutputStream(bos);
    java.io.ObjectOutputStream oos = new java.io.ObjectOutputStream(dos);
    oos.writeObject(cacheObj);
    oos.flush();
    dos.close();
    bos.flush();
    objData = bos.toByteArray();
    oos.close();
    bos.close();
    long after = System.currentTimeMillis();
    System.out.println("BeanUtils.toSerialized, t=" + (after - before) + " ms, (" + cacheObj + ") ratio=" + objData.length + "/" + bytes.length);
    return objData;
}

Example 35 with DeflaterOutputStream

use of java.util.zip.DeflaterOutputStream in project vcell by virtualcell.

the class VCellApiClient method toCompressedSerialized.

public static byte[] toCompressedSerialized(Serializable cacheObj) throws java.io.IOException {
    java.io.ByteArrayOutputStream bos = new java.io.ByteArrayOutputStream();
    DeflaterOutputStream dos = new DeflaterOutputStream(bos);
    java.io.ObjectOutputStream oos = new java.io.ObjectOutputStream(dos);
    oos.writeObject(cacheObj);
    oos.flush();
    dos.close();
    bos.flush();
    byte[] objData = bos.toByteArray();
    oos.close();
    bos.close();
    return objData;
}