Examples of org.dcm4che3.data.Fragments

org.dcm4che3.data.Fragments
@author Gunter Zeilinger

            Attributes frameFctGroups,
            int tag) {
        if (frameFctGroups == null) {
            return imgAttrs;
        }
        Attributes group = frameFctGroups.getNestedDataset(tag);
        if (group == null && sharedFctGroups != null) {
            group = sharedFctGroups.getNestedDataset(tag);
        }
        return group != null ? group : imgAttrs;
    }

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        dis = new DicomInputStream(new ImageInputStreamAdapter(iis));
        dis.setIncludeBulkData(IncludeBulkData.URI);
        dis.setBulkDataDescriptor(BulkDataDescriptor.PIXELDATA);
        dis.setURI("java:iis"); // avoid copy of pixeldata to temporary file
        Attributes fmi = dis.readFileMetaInformation();
        Attributes ds = dis.readDataset(-1, -1);
        metadata = new DicomMetaData(fmi, ds);
        Object pixeldata = ds.getValue(Tag.PixelData, pixeldataVR );
        if (pixeldata != null) {
            frames = ds.getInt(Tag.NumberOfFrames, 1);
            width = ds.getInt(Tag.Columns, 0);
            height = ds.getInt(Tag.Rows, 0);
            samples = ds.getInt(Tag.SamplesPerPixel, 1);
            banded = samples > 1 && ds.getInt(Tag.PlanarConfiguration, 0) != 0;
            bitsAllocated = ds.getInt(Tag.BitsAllocated, 8);
            bitsStored = ds.getInt(Tag.BitsStored, bitsAllocated);
            dataType = bitsAllocated <= 8 ? DataBuffer.TYPE_BYTE 
                                          : DataBuffer.TYPE_USHORT;
            pmi = PhotometricInterpretation.fromString(
                    ds.getString(Tag.PhotometricInterpretation, "MONOCHROME2"));
            if (pixeldata instanceof BulkData) {
                iis.setByteOrder(ds.bigEndian() 
                        ? ByteOrder.BIG_ENDIAN
                        : ByteOrder.LITTLE_ENDIAN);
                this.frameLength = pmi.frameLength(width, height, samples, bitsAllocated);
                this.pixeldata = (BulkData) pixeldata;
            } else {

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        }
    }


    private BulkData extractPixelData(BulkData src, int frame,
            int length) {
        return new BulkData(src.uriWithoutOffsetAndLength(),
                src.offset + frame * length, length,
                src.bigEndian);
    }

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        dataset.setBytes("PRIVATE", 0x00090002, VR.OB, BYTE01);
        dataset.setDouble(Tag.FrameTime, VR.DS, 33.0);
        dataset.setInt(Tag.SamplesPerPixel, VR.US, 1);
        dataset.setInt(Tag.NumberOfFrames, VR.IS, 1);
        dataset.setInt(Tag.FrameIncrementPointer, VR.AT, Tag.FrameTime);
        dataset.setValue(Tag.OverlayData, VR.OW, new BulkData(null, "file:/OverlayData", false));
        Fragments frags = dataset.newFragments(Tag.PixelData, VR.OB, 2);
        frags.add(null);
        frags.add(new BulkData(null, "file:/PixelData", false));
        StringWriter writer = new StringWriter();
        JsonGenerator gen = Json.createGenerator(writer);
        new JSONWriter(gen).write(dataset);
        gen.flush();
        assertEquals(RESULT, writer.toString());

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                    (byte[]) pixelData, frame, calcFrameLength(src)));
        } else if (pixelData instanceof BulkData) {
            dest.setValue(Tag.PixelData, vr.vr, extractPixelData(
                    (BulkData) pixelData, frame, calcFrameLength(src)));
        } else {
            Fragments destFrags = dest.newFragments(Tag.PixelData, vr.vr, 2);
            destFrags.add(null);
            destFrags.add(((Fragments) pixelData).get(frame + 1));
        }
    }

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        dataset.setDouble(Tag.FrameTime, VR.DS, 33.0);
        dataset.setInt(Tag.SamplesPerPixel, VR.US, 1);
        dataset.setInt(Tag.NumberOfFrames, VR.IS, 1);
        dataset.setInt(Tag.FrameIncrementPointer, VR.AT, Tag.FrameTime);
        dataset.setValue(Tag.OverlayData, VR.OW, new BulkData(null, "file:/OverlayData", false));
        Fragments frags = dataset.newFragments(Tag.PixelData, VR.OB, 2);
        frags.add(null);
        frags.add(new BulkData(null, "file:/PixelData", false));
        StringWriter writer = new StringWriter();
        JsonGenerator gen = Json.createGenerator(writer);
        new JSONWriter(gen).write(dataset);
        gen.flush();
        assertEquals(RESULT, writer.toString());

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        if (decompressor == null || super.tstype == TransferSyntaxType.RLE)
            bi = createBufferedImage(
                    Math.min(bitsStored, tstype.getMaxBitsStored()),
                    super.tstype == TransferSyntaxType.RLE || banded,
                    signed && tstype.canEncodeSigned());
        Fragments compressedPixeldata = 
                dataset.newFragments(Tag.PixelData, VR.OB, frames + 1);
        compressedPixeldata.add(Value.NULL);
        for (int i = 0; i < frames; i++) {
            CompressedFrame frame = new CompressedFrame(i);
            if (embeddedOverlays.length != 0)
                frame.compress();
            compressedPixeldata.add(frame);
        }
        if (samples > 1) {
            dataset.setString(Tag.PhotometricInterpretation, VR.CS, 
                    (decompressor != null ? pmi.decompress() : pmi)
                            .compress(tsuid).toString());

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        ds.setString(Tag.SOPClassUID, VR.UI, "1.2.3.4");
        ds.setString(Tag.SOPInstanceUID, VR.UI, "4.3.2.1");
        BulkData bdl = new BulkData(
                uri("OT-PAL-8-face"), 1654, 307200, false);
        ds.setValue(Tag.PixelData, VR.OW, bdl);
        Fragments frags = ds.newFragments("DicomOutputStreamTest", 0x99990010, VR.OB, 3);
        frags.add(null);
        frags.add(new byte[] { 1, 2, 3, 4 });
        frags.add(bdl);
        return ds;
    }

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                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) {

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        return attrs;
    }


    private void readFragments(Attributes attrs, int fragsTag, VR vr)
            throws IOException {
        Fragments frags = new Fragments(vr, attrs.bigEndian(), 10);
        String privateCreator = attrs.getPrivateCreator(fragsTag);
        for (int i = 0; true; ++i) {
            readHeader();
            if (tag == Tag.Item) {
                addItemPointer(fragsTag, privateCreator, i);
                handler.readValue(this, frags);
                removeItemPointer();
            } else if (tag == Tag.SequenceDelimitationItem) {
                if (length != 0)
                    skipAttribute(UNEXPECTED_NON_ZERO_ITEM_LENGTH);
                break;
            } else
                skipAttribute(UNEXPECTED_ATTRIBUTE);
        }
        if (frags.isEmpty())
            attrs.setNull(fragsTag, vr);
        else {
            frags.trimToSize();
            attrs.setValue(fragsTag, vr, frags);
        }
    }

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