Examples with BulkData org.dcm4che3.data.BulkData used on opensource projects

Example 11 with BulkData

use of org.dcm4che3.data.BulkData in project dcm4che by dcm4che.

the class DicomImageReader method initPixelDataIIS.

/**
 * Initializes the pixel data reading from an image input stream
 */
private void initPixelDataIIS(DicomInputStream dis) throws IOException {
    if (pixelDataLength == 0)
        return;
    if (pixelDataLength > 0) {
        pixelData = new BulkData("pixeldata://", dis.getPosition(), dis.length(), dis.bigEndian());
        metadata.getAttributes().setValue(Tag.PixelData, pixelDataVR, pixelData);
        return;
    }
    dis.readItemHeader();
    byte[] b = new byte[dis.length()];
    dis.readFully(b);
    long start = dis.getPosition();
    pixelDataFragments = new Fragments(pixelDataVR, dis.bigEndian(), frames);
    pixelDataFragments.add(b);
    generateOffsetLengths(pixelDataFragments, frames, b, start);
}

Example 12 with BulkData

use of org.dcm4che3.data.BulkData in project Weasis by nroduit.

the class RawImageIO method getDicomFile.

public File getDicomFile() {
    Attributes dcm = getDicomObject();
    File file = imageCV.getFile();
    BulkData bdl = new BulkData(file.toURI().toString(), FileRawImage.HEADER_LENGTH, (int) file.length() - FileRawImage.HEADER_LENGTH, false);
    dcm.setValue(Tag.PixelData, VR.OW, bdl);
    File tmpFile = new File(DicomMediaIO.DICOM_EXPORT_DIR, dcm.getString(Tag.SOPInstanceUID));
    try (DicomOutputStream out = new DicomOutputStream(tmpFile)) {
        out.writeDataset(dcm.createFileMetaInformation(UID.ImplicitVRLittleEndian), dcm);
    } catch (IOException e) {
        LOGGER.error("Cannot write dicom file", e);
        return null;
    }
    return tmpFile;
}

Example 13 with BulkData

use of org.dcm4che3.data.BulkData in project dcm4che by dcm4che.

the class SAXWriter method writeAttribute.

private void writeAttribute(Value value, boolean bigEndian) throws SAXException {
    if (value.isEmpty())
        return;
    if (value instanceof Sequence) {
        Sequence seq = (Sequence) value;
        int number = 0;
        for (Attributes item : seq) {
            startElement("Item", "number", ++number);
            writeItem(item);
            endElement("Item");
        }
    } else if (value instanceof Fragments) {
        Fragments frags = (Fragments) value;
        int number = 0;
        for (Object frag : frags) {
            ++number;
            if (frag instanceof Value && ((Value) frag).isEmpty())
                continue;
            startElement("DataFragment", "number", number);
            if (frag instanceof BulkData)
                writeBulkData((BulkData) frag);
            else {
                byte[] b = (byte[]) frag;
                if (bigEndian)
                    frags.vr().toggleEndian(b, true);
                writeInlineBinary(b);
            }
            endElement("DataFragment");
        }
    } else if (value instanceof BulkData) {
        writeBulkData((BulkData) value);
    }
}

Example 14 with BulkData

use of org.dcm4che3.data.BulkData in project dcm4che by dcm4che.

the class StreamSegment method getSegments.

private static long[][] getSegments(SegmentedInputImageStream iis) throws IOException {
    Integer curSegment = iis.getCurSegment();
    if (curSegment != null && curSegment >= 0) {
        ImageDescriptor desc = iis.getImageDescriptor();
        List<Object> fragments = iis.getFragments();
        Integer lastSegment = iis.getLastSegment();
        if (!desc.isMultiframe() && lastSegment < fragments.size()) {
            lastSegment = fragments.size();
        }
        long[] segPositions = new long[lastSegment - curSegment];
        long[] segLength = new long[segPositions.length];
        long beforePos = 0;
        for (int i = curSegment; i < lastSegment; i++) {
            synchronized (fragments) {
                if (i < fragments.size()) {
                    Object fragment = fragments.get(i);
                    int k = i - curSegment;
                    if (fragment instanceof BulkData) {
                        BulkData bulk = (BulkData) fragment;
                        segPositions[k] = bulk.offset();
                        segLength[k] = bulk.length();
                    } else {
                        byte[] byteFrag = (byte[]) fragment;
                        segPositions[k] = beforePos;
                        segLength[k] = byteFrag.length;
                    }
                    beforePos += segLength[k] & 0xFFFFFFFFl;
                }
            }
        }
        return new long[][] { segPositions, segLength };
    }
    return null;
}

Example 15 with BulkData

use of org.dcm4che3.data.BulkData in project dcm4che by dcm4che.

the class DicomImageReader method generateOffsetLengths.

/**
 * Creates an offset/length table based on the frame positions
 */
public static void generateOffsetLengths(Fragments pixelData, int frames, byte[] basicOffsetTable, long start) {
    long lastOffset = 0;
    BulkData lastFrag = null;
    for (int frame = 0; frame < frames; frame++) {
        long offset = frame > 0 ? 1 : 0;
        int offsetStart = frame * 4;
        if (basicOffsetTable.length >= offsetStart + 4) {
            offset = ByteUtils.bytesToIntLE(basicOffsetTable, offsetStart);
            if (offset != 1) {
                // Handle > 4 gb total image size by assuming incrementing modulo 4gb
                offset = offset | (lastOffset & 0xFFFFFF00000000l);
                if (offset < lastOffset)
                    offset += 0x100000000l;
                lastOffset = offset;
                LOG.trace("Found offset {} for frame {}", offset, frame);
            }
        }
        long position = -1;
        if (offset != 1) {
            position = start + offset + 8;
        }
        BulkData frag = new BulkData("compressedPixelData://", position, -1, false);
        if (lastFrag != null && position != -1) {
            lastFrag.setLength(position - 8 - lastFrag.offset());
        }
        lastFrag = frag;
        pixelData.add(frag);
        if (offset == 0 && frame > 0) {
            start = -1;
        }
    }
}