Examples of org.dcm4che3.data.Fragments

org.dcm4che3.image.LookupTableFactory
@author Gunter Zeilinger

                write(item);
            }
            gen.writeEnd();
        } else if (value instanceof Fragments) {
            gen.writeStartArray("DataFragment");
            Fragments frags = (Fragments) value;
            for (Object frag : frags) {
                gen.writeStartObject();
                if (!(frag instanceof Value && ((Value) frag).isEmpty())) 
                    if (frag instanceof BulkData)
                        writeBulkData((BulkData) frag);
                    else {
                        writeInlineBinary(frags.vr(), (byte[]) frag, bigEndian, true);
                    }
                gen.writeEnd();
            }
            gen.writeEnd();
        } else if (value instanceof BulkData) {

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    private void readDataFragment(Attributes attrs, int tag, VR vr) {
        if (next() != Event.START_ARRAY) {
            throw new JsonParsingException("Unexpected " + event
                    + ", expected array of data fragment objects", location);
        }
        Fragments frags = attrs.newFragments(tag, vr, 10);
        for (;;) {
            switch (next()) {
            case END_ARRAY:
                frags.trimToSize();
                return;
            case VALUE_NULL:
                frags.add(null);
                break;
            case START_OBJECT:
                frags.add(readDataFragment(attrs.bigEndian()));
                break;
            default:
                throw new JsonParsingException("Unexpected " + event 
                        + ", expected data fragment object", location);
            }

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        }
    }


    private Sequence refSOPSeq(String studyIUID, String seriesIUID) {
        Attributes refStudy = getOrAddItem(evidenceSeq, Tag.StudyInstanceUID, studyIUID);
        Sequence refSeriesSeq = refStudy.ensureSequence(Tag.ReferencedSeriesSequence, 10);
        Attributes refSeries = getOrAddItem(refSeriesSeq,Tag.SeriesInstanceUID, seriesIUID);
        return refSeries.ensureSequence(Tag.ReferencedSOPSequence, 100);
    }

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    public Attributes makeActionInfo(List<String> refSOPs) {
        Attributes actionInfo = new Attributes(2);
        actionInfo.setString(Tag.TransactionUID, VR.UI, UIDUtils.createUID());
        int n = refSOPs.size() / 2;
        Sequence refSOPSeq = actionInfo.newSequence(Tag.ReferencedSOPSequence, n);
        for (int i = 0, j = 0; j < n; j++) {
            Attributes refSOP = new Attributes(2);
            refSOP.setString(Tag.ReferencedSOPClassUID, VR.UI, refSOPs.get(i++));
            refSOP.setString(Tag.ReferencedSOPInstanceUID, VR.UI, refSOPs.get(i++));
            refSOPSeq.add(refSOP);
        }
        return actionInfo;
    }

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        adjustReferencedImages(dest, Tag.SourceImageSequence);
        return dest;
    }


    private void adjustReferencedImages(Attributes attrs, int sqtag) {
        Sequence sq = attrs.getSequence(sqtag);
        if (sq == null)
            return;
        
        ArrayList<Attributes> newRefs = new ArrayList<Attributes>();
        for (Iterator<Attributes> itr = sq.iterator(); itr.hasNext();) {
            Attributes ref = (Attributes) itr.next();
            String cuid = legacySOPClassUID(ref.getString(Tag.ReferencedSOPClassUID));
            if (cuid == null)
                continue;


            itr.remove();
            String iuid = uidMapper.get(ref.getString(Tag.ReferencedSOPInstanceUID));
            int[] frames = ref.getInts(Tag.ReferencedFrameNumber);
            int n = frames == null ? nofAccessor.getNumberOfFrames(iuid)
                                   : frames.length;
            ref.remove(Tag.ReferencedFrameNumber);
            ref.setString(Tag.ReferencedSOPClassUID, VR.UI, cuid);
            for (int i = 0; i < n; i++) {
                Attributes newRef = new Attributes(ref);
                newRef.setString(Tag.ReferencedSOPInstanceUID, VR.UI,
                        iuid + '.' + (frames != null ? frames[i] : (i+1)));
                newRefs.add(newRef);
            }
        }
        for (Attributes ref : newRefs)
            sq.add(ref);
    }

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        String layerName = psAttrs.getString(tagOverlayActivationLayer);
        if (layerName == null)
            throw new IllegalArgumentException("Missing "
                    + TagUtils.toString(tagOverlayActivationLayer)
                    + " Overlay Activation Layer");
        Sequence layers = psAttrs.getSequence(Tag.GraphicLayerSequence);
        if (layers == null)
            throw new IllegalArgumentException("Missing "
                    + TagUtils.toString(Tag.GraphicLayerSequence)
                    + " Graphic Layer Sequence");

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        }
        return group != null ? group : imgAttrs;
    }


    private Attributes selectVOILUT(Attributes psAttrs, String iuid, int frame) {
        Sequence voiLUTs = psAttrs.getSequence(Tag.SoftcopyVOILUTSequence);
        if (voiLUTs != null)
            for (Attributes voiLUT : voiLUTs) {
                Sequence refImgs = voiLUT.getSequence(Tag.ReferencedImageSequence);
                if (refImgs == null || refImgs.isEmpty())
                    return voiLUT;
                for (Attributes refImg : refImgs) {
                    if (iuid.equals(refImg.getString(Tag.ReferencedSOPInstanceUID))) {
                        int[] refFrames = refImg.getInts(Tag.ReferencedFrameNumber);
                        if (refFrames == null)

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        DicomInputStream dis = null;
        try {
            System.out.print("Validate: " + file + " ... ");
            dis = new DicomInputStream(file);
            Attributes attrs = dis.readDataset(-1, -1);
            ValidationResult result = attrs.validate(iod);
            if (result.isValid())
                System.out.println("OK");
            else {
                System.out.println("FAILED:");
                System.out.println(result.asText(attrs));
            }
        } catch (IOException e) {
            System.out.println("FAILED: " + e.getMessage());
        } finally {
            SafeClose.close(dis);

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                    dParam.isPreferWindow());
            if (dParam.isAutoWindowing())
                lutParam.autoWindowing(imgAttrs, raster);
            lutParam.setPresentationLUT(imgAttrs);
        }
        LookupTable lut = lutParam.createLUT(outBits);
        lut.lookup(raster, destRaster);
        return destRaster;
    }

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                sm.getDataType() == raster.getSampleModel().getDataType()
                        ? raster
                        : Raster.createWritableRaster(sm, null);
        Attributes imgAttrs = metadata.getAttributes();
        StoredValue sv = StoredValue.valueOf(imgAttrs);
        LookupTableFactory lutParam = new LookupTableFactory(sv);
        DicomImageReadParam dParam = param instanceof DicomImageReadParam
                ? (DicomImageReadParam) param
                : new DicomImageReadParam();
        Attributes psAttrs = dParam.getPresentationState();
        if (psAttrs != null) {
            lutParam.setModalityLUT(psAttrs);
            lutParam.setVOI(
                    selectVOILUT(psAttrs,
                            imgAttrs.getString(Tag.SOPInstanceUID),
                            frameIndex+1),
                    0, 0, false);
            lutParam.setPresentationLUT(psAttrs);
        } else {
            Attributes sharedFctGroups = imgAttrs.getNestedDataset(
                    Tag.SharedFunctionalGroupsSequence);
            Attributes frameFctGroups = imgAttrs.getNestedDataset(
                    Tag.PerFrameFunctionalGroupsSequence, frameIndex);
            lutParam.setModalityLUT(
                    selectFctGroup(imgAttrs, sharedFctGroups, frameFctGroups,
                            Tag.PixelValueTransformationSequence));
            if (dParam.getWindowWidth() != 0) {
                lutParam.setWindowCenter(dParam.getWindowCenter());
                lutParam.setWindowWidth(dParam.getWindowWidth());
            } else
                lutParam.setVOI(
                    selectFctGroup(imgAttrs, sharedFctGroups, frameFctGroups,
                            Tag.FrameVOILUTSequence),
                    dParam.getWindowIndex(),
                    dParam.getVOILUTIndex(),
                    dParam.isPreferWindow());
            if (dParam.isAutoWindowing())
                lutParam.autoWindowing(imgAttrs, raster);
            lutParam.setPresentationLUT(imgAttrs);
        }
        LookupTable lut = lutParam.createLUT(outBits);
        lut.lookup(raster, destRaster);
        return destRaster;
    }

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