Examples of org.dcm4che3.data.Sequence

org.dcm4che3.io.DicomInputStream
@author Gunter Zeilinger

        return true;
    }


    private Attributes createIAN(Attributes inst) {
        Attributes ian = new Attributes(3);
        Sequence refPpsSeq =
                ian.newSequence(Tag.ReferencedPerformedProcedureStepSequence, 1);
        if (refPpsIUID != null) {
            Attributes refPps = new Attributes(3);
            refPps.setString(Tag.ReferencedSOPClassUID, VR.UI, refPpsCUID);
            refPps.setString(Tag.ReferencedSOPInstanceUID, VR.UI, refPpsIUID);
            refPps.setNull(Tag.PerformedWorkitemCodeSequence,VR.SQ); 
            refPpsSeq.add(refPps);
        }
        ian.newSequence(Tag.ReferencedSeriesSequence, 1);
        ian.setString(Tag.StudyInstanceUID, VR.UI,
                inst.getString(Tag.StudyInstanceUID));
        return ian ;

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                inst.getString(Tag.StudyInstanceUID));
        return ian ;
    }


    private void updateIAN(Attributes mpps, Attributes inst) {
        Sequence refSeriesSeq = mpps.getSequence(Tag.ReferencedSeriesSequence);
        Attributes refSeries = getRefSeries(refSeriesSeq, inst);
        Sequence refSOPSeq = refSeries.getSequence(Tag.ReferencedSOPSequence);
        Attributes refSOP = new Attributes(6);
        refSOP.setString(Tag.RetrieveAETitle, VR.AE, getRetrieveAET());
        refSOP.setString(Tag.InstanceAvailability, VR.CS, availability);
        refSOP.setString(Tag.ReferencedSOPClassUID, VR.UI,
                inst.getString(Tag.SOPClassUID));
        refSOP.setString(Tag.ReferencedSOPInstanceUID, VR.UI,
                inst.getString(Tag.SOPInstanceUID));
        if (retrieveURI != null)
            refSOP.setString(Tag.RetrieveURI, VR.UT, retrieveURI);
        if (retrieveUID != null)
            refSOP.setString(Tag.RetrieveLocationUID, VR.UI, retrieveUID);
        refSOPSeq.add(refSOP);
    }

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    public static void addAttributes(Attributes attrs, int[] tags, String... ss) {
        Attributes item = attrs;
        for (int i = 0; i < tags.length-1; i++) {
            int tag = tags[i];
            Sequence sq = item.getSequence(tag);
            if (sq == null)
                sq = item.newSequence(tag, 1);
            if (sq.isEmpty())
                sq.add(new Attributes());
            item = sq.get(0);
        }
        int tag = tags[tags.length-1];
        VR vr = ElementDictionary.vrOf(tag,
                item.getPrivateCreator(tag));
        if (ss.length == 0)

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        mpps.setString(Tag.PerformedProcedureStepEndDate, VR.DA,
                mpps.getString(Tag.PerformedProcedureStepStartDate));
        mpps.setString(Tag.PerformedProcedureStepEndTime, VR.TM,
                mpps.getString(Tag.PerformedProcedureStepStartTime));
        mpps.setString(Tag.PerformedProcedureStepStatus, VR.CS, finalStatus);
        Sequence dcrSeq = mpps.newSequence(Tag.PerformedProcedureStepDiscontinuationReasonCodeSequence, 1);
        if (discontinuationReason != null)
            dcrSeq.add(new Attributes(discontinuationReason));


        Sequence raSeq = inst.getSequence(Tag.RequestAttributesSequence);
        if (raSeq == null || raSeq.isEmpty()) {
            Sequence ssaSeq = 
                    mpps.newSequence(Tag.ScheduledStepAttributesSequence, 1);
            Attributes ssa = new Attributes();
            ssaSeq.add(ssa);
            for (int tag : SSA_TYPE_2_ATTRS)
                ssa.setNull(tag, dict.vrOf(tag));
            ssa.addSelected(inst, SSA_ATTRS);
        } else {
            Sequence ssaSeq =
                    mpps.newSequence(Tag.ScheduledStepAttributesSequence, raSeq.size());
            for (Attributes ra : raSeq) {
                Attributes ssa = new Attributes();
                ssaSeq.add(ssa);
                for (int tag : SSA_TYPE_2_ATTRS)
                    ssa.setNull(tag, dict.vrOf(tag));
                ssa.addSelected(inst, SSA_ATTRS);
                ssa.addSelected(ra, SSA_ATTRS);
            }

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                if (Status.isPending(status)) {
                    if (returnTag != null) {


                        if (returnTag.equals(Tag.OtherPatientIDsSequence))
                        {
                            Sequence seq = data.getSequence(returnTag);
                            for (Attributes element : seq)
                            {
                                String returnedValue = element.getString(Tag.PatientID);
                                if (!returnedValues.contains(returnedValue))
                                    returnedValues.add(returnedValue);

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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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        imageReader.setInput(iis);
        return imageReader.read(frame-1, readParam());
    }


    private ImageReadParam readParam() {
        DicomImageReadParam param =
                (DicomImageReadParam) imageReader.getDefaultReadParam();
        param.setWindowCenter(windowCenter);
        param.setWindowWidth(windowWidth);
        param.setAutoWindowing(autoWindowing);
        param.setWindowIndex(windowIndex);
        param.setVOILUTIndex(voiLUTIndex);
        param.setPreferWindow(preferWindow);
        param.setPresentationState(prState);
        param.setOverlayActivationMask(overlayActivationMask);
        param.setOverlayGrayscaleValue(overlayGrayscaleValue);
        return param;
    }

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            main.setEncodingOptions(CLIUtils.encodingOptionsOf(cl));
            try {
                if (cl.hasOption("i")) {
                    String fname = cl.getOptionValue("i");
                    if (fname.equals("-")) {
                        main.parse(new DicomInputStream(System.in));
                    } else {
                        DicomInputStream dis = 
                                new DicomInputStream(new File(fname));
                        try {
                            main.parse(dis);
                        } finally {
                            dis.close();
                        }
                    }
                }


                if (cl.hasOption("j"))

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        if (!from.renameTo(dest))
            throw new IOException("Failed to rename " + from + " to " + dest);
    }


    private static Attributes parse(File file) throws IOException {
        DicomInputStream in = new DicomInputStream(file);
        try {
            in.setIncludeBulkData(IncludeBulkData.NO);
            return in.readDataset(-1, Tag.PixelData);
        } finally {
            SafeClose.close(in);
        }
    }

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    }


    private static Attributes loadDicomObject(File f) throws IOException {
        if (f == null)
            return null;
        DicomInputStream dis = new DicomInputStream(f);
        try {
            return dis.readDataset(-1, -1);
        } finally {
            SafeClose.close(dis);
        }
    }

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