Package org.dcm4che3.media

Examples of org.dcm4che3.media.DicomDirWriter

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        // by including the keyword/tag value of the sequence attribute,
        // e.g. 00400275/00400009 for Scheduled Procedure Step ID in
        // the Request Attributes Sequence.

        String[] attributes = new String[0];
        main.setAttributes(new Attributes());
        CLIUtils.addAttributes(main.getAttributes(), attributes);

        // scan
        t1 = System.currentTimeMillis();
        main.scanFiles(Arrays.asList(file.getAbsolutePath()), false); // do not
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            throw new IllegalStateException("IOD net initialized");
        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));
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                    "Unsupported SOP Class: " + mfcuid);
        return impl;
    }

    private Attributes extract(Attributes emf, int frame, String cuid) {
        Attributes sfgs = emf.getNestedDataset(Tag.SharedFunctionalGroupsSequence);
        if (sfgs == null)
            throw new IllegalArgumentException(
                    "Missing (5200,9229) Shared Functional Groups Sequence");
        Attributes fgs = emf.getNestedDataset(Tag.PerFrameFunctionalGroupsSequence, frame);
        if (fgs == null)
            throw new IllegalArgumentException(
                    "Missing (5200,9230) Per-frame Functional Groups Sequence Item for frame #" + (frame + 1));
        Attributes dest = new Attributes(emf.size() * 2);
        dest.addNotSelected(emf, EXCLUDE_TAGS);
        addFunctionGroups(dest, sfgs);
        addFunctionGroups(dest, fgs);
        addPixelData(dest, emf, frame);
        dest.setString(Tag.SOPClassUID, VR.UI, cuid);
        dest.setString(Tag.SOPInstanceUID, VR.UI, uidMapper.get(
                dest.getString(Tag.SOPInstanceUID)) + '.' + (frame + 1));
        dest.setString(Tag.InstanceNumber, VR.IS,
                createInstanceNumber(dest.getString(Tag.InstanceNumber, ""), frame));
        dest.setString(Tag.ImageType, VR.CS, dest.getStrings(Tag.FrameType));
        dest.remove(Tag.FrameType);
        if (!preserveSeriesInstanceUID)
            dest.setString(Tag.SeriesInstanceUID, VR.UI, uidMapper.get(
                    dest.getString(Tag.SeriesInstanceUID)));
        adjustReferencedImages(dest, Tag.ReferencedImageSequence);
        adjustReferencedImages(dest, Tag.SourceImageSequence);
        return dest;
    }
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        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)
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            sq.add(ref);
    }

    private void addFunctionGroups(Attributes dest, Attributes fgs) {
        dest.addSelected(fgs, Tag.ReferencedImageSequence);
        Attributes fg;
        for (int sqTag : fgs.tags())
            if (sqTag != Tag.ReferencedImageSequence
                    && (fg = fgs.getNestedDataset(sqTag)) != null)
                dest.addAll(fg);
    }
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                + "{\"BulkDataURI\":\"file:/PixelData\"}"
            + "]}}";

    @Test
    public void test() {
        Attributes dataset = new Attributes();
        dataset.setString(Tag.SpecificCharacterSet, VR.CS, null, "ISO 2022 IR 87");
        dataset.setString(Tag.ImageType, VR.CS, "DERIVED", "PRIMARY");
        Attributes item = new Attributes(2);
        dataset.newSequence(Tag.SourceImageSequence, 1).add(item);
        item.setString(Tag.ReferencedSOPClassUID, VR.UI, UID.CTImageStorage);
        item.setString(Tag.ReferencedSOPInstanceUID, VR.UI, "1.2.3.4");
        dataset.setString(Tag.PatientName, VR.PN, "af^ag=if^ig=pf^pg");
        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);
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        }
        return new BufferedImage(cm, raster , false, null);
    }

    private byte[] extractOverlay(int gg0000, WritableRaster raster) {
        Attributes attrs = metadata.getAttributes();

        if (attrs.getInt(Tag.OverlayBitsAllocated | gg0000, 1) == 1)
            return null;

        int ovlyRows = attrs.getInt(Tag.OverlayRows | gg0000, 0);
        int ovlyColumns = attrs.getInt(Tag.OverlayColumns | gg0000, 0);
        int bitPosition = attrs.getInt(Tag.OverlayBitPosition | gg0000, 0);

        int mask = 1<<bitPosition;
        int length = ovlyRows * ovlyColumns;

        byte[] ovlyData = new byte[(((length+7)>>>3)+1)&(~1)] ;
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                : siis;
    }

    private void applyOverlay(int gg0000, WritableRaster raster,
            int frameIndex, ImageReadParam param, int outBits, byte[] ovlyData) {
        Attributes ovlyAttrs = metadata.getAttributes();
        int grayscaleValue = 0xffff;
        if (param instanceof DicomImageReadParam) {
            DicomImageReadParam dParam = (DicomImageReadParam) param;
            Attributes psAttrs = dParam.getPresentationState();
            if (psAttrs != null) {
                if (psAttrs.containsValue(Tag.OverlayData | gg0000))
                    ovlyAttrs = psAttrs;
                grayscaleValue = Overlays.getRecommendedDisplayGrayscaleValue(
                        psAttrs, gg0000);
            } else
                grayscaleValue = dParam.getOverlayGrayscaleValue();
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    }

    private int[] getActiveOverlayGroupOffsets(ImageReadParam param) {
        if (param instanceof DicomImageReadParam) {
            DicomImageReadParam dParam = (DicomImageReadParam) param;
            Attributes psAttrs = dParam.getPresentationState();
            if (psAttrs != null)
                return Overlays.getActiveOverlayGroupOffsets(psAttrs);
            else
                return Overlays.getActiveOverlayGroupOffsets(
                        metadata.getAttributes(),
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            int frameIndex, ImageReadParam param, SampleModel sm, int outBits) {
         WritableRaster destRaster =
                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) {
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