Examples with ImageDescriptor org.dcm4che3.imageio.codec.ImageDescriptor used on opensource projects

Example 11 with ImageDescriptor

use of org.dcm4che3.imageio.codec.ImageDescriptor in project dcm4che by dcm4che.

the class NativeImageReader method getNativeImage.

private PlanarImage getNativeImage(ImageReadParam param) throws IOException {
    StreamSegment seg = StreamSegment.getStreamSegment(iis, param);
    ImageDescriptor desc = seg.getImageDescriptor();
    int dcmFlags = (canEncodeSigned && desc.isSigned()) ? Imgcodecs.DICOM_FLAG_SIGNED : Imgcodecs.DICOM_FLAG_UNSIGNED;
    if (ybr2rgb(desc.getPhotometricInterpretation())) {
        dcmFlags |= Imgcodecs.DICOM_FLAG_YBR;
    }
    if (seg instanceof FileStreamSegment) {
        MatOfDouble positions = null;
        MatOfDouble lengths = null;
        try {
            positions = new MatOfDouble(ExtendSegmentedInputImageStream.getDoubleArray(seg.getSegPosition()));
            lengths = new MatOfDouble(ExtendSegmentedInputImageStream.getDoubleArray(seg.getSegLength()));
            return ImageCV.toImageCV(Imgcodecs.dicomJpgFileRead(((FileStreamSegment) seg).getFilePath(), positions, lengths, dcmFlags, Imgcodecs.IMREAD_UNCHANGED));
        } finally {
            closeMat(positions);
            closeMat(lengths);
        }
    } else if (seg instanceof MemoryStreamSegment) {
        Mat buf = null;
        try {
            ByteBuffer b = ((MemoryStreamSegment) seg).getCache();
            buf = new Mat(1, b.limit(), CvType.CV_8UC1);
            buf.put(0, 0, b.array());
            return ImageCV.toImageCV(Imgcodecs.dicomJpgMatRead(buf, dcmFlags, Imgcodecs.IMREAD_UNCHANGED));
        } finally {
            closeMat(buf);
        }
    }
    return null;
}

Example 12 with ImageDescriptor

use of org.dcm4che3.imageio.codec.ImageDescriptor in project dcm4che by dcm4che.

the class NativeJ2kImageWriter method write.

@Override
public void write(IIOMetadata streamMetadata, IIOImage image, ImageWriteParam param) throws IOException {
    if (output == null) {
        throw new IllegalStateException("input cannot be null");
    }
    if (!(output instanceof ImageOutputStream)) {
        throw new IllegalArgumentException("input is not an ImageInputStream!");
    }
    ImageOutputStream stream = (ImageOutputStream) output;
    stream.setByteOrder(ByteOrder.LITTLE_ENDIAN);
    J2kImageWriteParam j2kParams = (J2kImageWriteParam) param;
    if (!(stream instanceof BytesWithImageImageDescriptor)) {
        throw new IllegalArgumentException("stream does not implement BytesWithImageImageDescriptor!");
    }
    ImageDescriptor desc = ((BytesWithImageImageDescriptor) stream).getImageDescriptor();
    RenderedImage renderedImage = image.getRenderedImage();
    Mat buf = null;
    MatOfInt dicomParams = null;
    try {
        ImageCV mat = null;
        try {
            // Band interleaved mode (PlanarConfiguration = 1) is converted to pixel interleaved
            // So the input image has always a pixel interleaved mode mode((PlanarConfiguration = 0)
            mat = ImageConversion.toMat(renderedImage, param.getSourceRegion(), false);
            int cvType = mat.type();
            int channels = CvType.channels(cvType);
            boolean signed = desc.isSigned();
            int dcmFlags = signed ? Imgcodecs.DICOM_FLAG_SIGNED : Imgcodecs.DICOM_FLAG_UNSIGNED;
            int[] params = new int[16];
            // Image flags
            params[Imgcodecs.DICOM_PARAM_IMREAD] = Imgcodecs.IMREAD_UNCHANGED;
            // DICOM flags
            params[Imgcodecs.DICOM_PARAM_DCM_IMREAD] = dcmFlags;
            // Image width
            params[Imgcodecs.DICOM_PARAM_WIDTH] = mat.width();
            // Image height
            params[Imgcodecs.DICOM_PARAM_HEIGHT] = mat.height();
            // Type of compression
            params[Imgcodecs.DICOM_PARAM_COMPRESSION] = Imgcodecs.DICOM_CP_J2K;
            // Number of components
            params[Imgcodecs.DICOM_PARAM_COMPONENTS] = channels;
            // Bits per sample
            params[Imgcodecs.DICOM_PARAM_BITS_PER_SAMPLE] = desc.getBitsCompressed();
            // Interleave mode
            params[Imgcodecs.DICOM_PARAM_INTERLEAVE_MODE] = Imgcodecs.ILV_SAMPLE;
            // JPEG-2000 lossy ratio factor
            params[Imgcodecs.DICOM_PARAM_J2K_COMPRESSION_FACTOR] = j2kParams.getCompressionRatiofactor();
            dicomParams = new MatOfInt(params);
            buf = Imgcodecs.dicomJpgWrite(mat, dicomParams, "");
            if (buf.empty()) {
                throw new IIOException("Native JPEG2000 encoding error: null image");
            }
        } finally {
            if (mat != null) {
                mat.release();
            }
        }
        byte[] bSrcData = new byte[buf.width() * buf.height() * (int) buf.elemSize()];
        buf.get(0, 0, bSrcData);
        stream.write(bSrcData);
    } catch (Throwable t) {
        throw new IIOException("Native JPEG2000 encoding error", t);
    } finally {
        NativeImageReader.closeMat(dicomParams);
        NativeImageReader.closeMat(buf);
    }
}

Example 13 with ImageDescriptor

use of org.dcm4che3.imageio.codec.ImageDescriptor in project dcm4che by dcm4che.

the class DicomImageReader method initPixelDataFromAttributes.

private void initPixelDataFromAttributes(Attributes ds) {
    VR.Holder holder = new VR.Holder();
    Object value = ds.getValue(Tag.PixelData, holder);
    if (value != null) {
        imageDescriptor = new ImageDescriptor(ds);
        pixelDataVR = holder.vr;
        if (value instanceof BulkData) {
            pixelData = (BulkData) value;
            pixelDataLength = pixelData.length();
        } else if (value instanceof byte[]) {
            pixeldataBytes = (byte[]) value;
            pixelDataLength = pixeldataBytes.length;
        } else {
            // value instanceof Fragments
            pixelDataFragments = (Fragments) value;
            pixelDataLength = -1;
        }
    }
}