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

Example 1 with VR

use of org.dcm4che3.data.VR in project karnak by OsiriX-Foundation.

the class Profile method applyAction.

public void applyAction(Attributes dcm, Attributes dcmCopy, HMAC hmac, ProfileItem profilePassedInSequence, ActionItem actionPassedInSequence, AttributeEditorContext context) {
    for (int tag : dcm.tags()) {
        VR vr = dcm.getVR(tag);
        final ExprCondition exprCondition = new ExprCondition(dcmCopy);
        ActionItem currentAction = null;
        ProfileItem currentProfile = null;
        for (ProfileItem profileEntity : profiles.stream().filter(p -> !(p instanceof CleanPixelData)).collect(Collectors.toList())) {
            currentProfile = profileEntity;
            if (profileEntity.getCondition() == null || profileEntity.getCodeName().equals(ProfileItemType.DEFACING.getClassAlias()) || profileEntity.getCodeName().equals(ProfileItemType.CLEAN_PIXEL_DATA.getClassAlias())) {
                currentAction = profileEntity.getAction(dcm, dcmCopy, tag, hmac);
            } else {
                boolean conditionIsOk = (Boolean) ExpressionResult.get(profileEntity.getCondition(), exprCondition, Boolean.class);
                if (conditionIsOk) {
                    currentAction = profileEntity.getAction(dcm, dcmCopy, tag, hmac);
                }
            }
            if (currentAction != null) {
                break;
            }
            if (profileEntity.equals(profilePassedInSequence)) {
                currentAction = actionPassedInSequence;
                break;
            }
        }
        if (!(currentAction instanceof Remove) && !(currentAction instanceof ReplaceNull) && vr == VR.SQ) {
            final ProfileItem finalCurrentProfile = currentProfile;
            final ActionItem finalCurrentAction = currentAction;
            Sequence seq = dcm.getSequence(tag);
            if (seq != null) {
                for (Attributes d : seq) {
                    applyAction(d, dcmCopy, hmac, finalCurrentProfile, finalCurrentAction, context);
                }
            }
        } else {
            if (currentAction != null) {
                try {
                    currentAction.execute(dcm, tag, hmac);
                } catch (final Exception e) {
                    LOGGER.error("Cannot execute the currentAction {} for tag: {}", currentAction, TagUtils.toString(tag), e);
                }
            }
        }
    }
}

Example 2 with VR

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

the class PlanarConfig method processFile.

private char processFile(File file) {
    try {
        Attributes dataset;
        WritePlanarConfiguration writePlanarConfiguration = new WritePlanarConfiguration();
        try (DicomInputStream is = new DicomInputStream(file)) {
            is.setIncludeBulkData(DicomInputStream.IncludeBulkData.URI);
            is.setDicomInputHandler(writePlanarConfiguration);
            dataset = is.readDataset();
        }
        VR.Holder vr = new VR.Holder();
        Object value = dataset.getValue(Tag.PixelData, vr);
        if (value == null) {
            skipped++;
            return 'p';
        }
        ColorPMI colorPMI;
        try {
            colorPMI = ColorPMI.valueOf(dataset.getString(Tag.PhotometricInterpretation));
        } catch (IllegalArgumentException e) {
            skipped++;
            return 'm';
        }
        if (!(value instanceof BulkData)) {
            skipped++;
            return 'c';
        }
        int pc;
        try (RandomAccessFile raf = new RandomAccessFile(file, "rw")) {
            pc = planarConfiguration(file, raf, (BulkData) value, dataset, colorPMI);
            if (pc == dataset.getInt(Tag.PlanarConfiguration, 0)) {
                correct[pc]++;
                return CORRECT_CH[pc];
            }
            if (fix[pc]) {
                writePlanarConfiguration.writeTo(raf, pc);
            }
        }
        wrong[pc]++;
        if (uids && (fix[pc] || !fix[1 - pc]))
            uidslog().println(dataset.getString(Tag.SOPInstanceUID));
        return WRONG_CH[pc];
    } catch (IOException e) {
        System.err.println("Failed to update " + file + ':');
        e.printStackTrace(System.err);
        failed++;
    }
    return 'E';
}

Example 3 with VR

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

the class SAXWriter method writeValues.

private void writeValues(VR vr, Object val, boolean bigEndian, SpecificCharacterSet cs) throws SAXException {
    if (vr.isStringType())
        val = vr.toStrings(val, bigEndian, cs);
    int vm = vr.vmOf(val);
    for (int i = 0; i < vm; i++) {
        String s = vr.toString(val, bigEndian, i, null);
        addAttribute("number", Integer.toString(i + 1));
        if (vr == VR.PN) {
            PersonName pn = new PersonName(s, true);
            startElement("PersonName");
            writePNGroup("Alphabetic", pn, PersonName.Group.Alphabetic);
            writePNGroup("Ideographic", pn, PersonName.Group.Ideographic);
            writePNGroup("Phonetic", pn, PersonName.Group.Phonetic);
            endElement("PersonName");
        } else {
            startElement("Value");
            if (s != null)
                writeText(s);
            endElement("Value");
        }
    }
}

Example 4 with VR

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

the class DicomFileDetector method isEVR.

private static boolean isEVR(byte[] b134, int rlen) {
    int tagLE = ByteUtils.bytesToTagLE(b134, 0);
    int tagBE = ByteUtils.bytesToTagBE(b134, 0);
    VR vr = VR.valueOf(ByteUtils.bytesToVR(b134, 4));
    return vr != null && vr == ElementDictionary.getStandardElementDictionary().vrOf(tagLE >= 0 && tagLE < tagBE ? tagLE : tagBE);
}

Example 5 with VR

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

the class JSONWriter method readValue.

@Override
public void readValue(DicomInputStream dis, Attributes attrs) throws IOException {
    int tag = dis.tag();
    VR vr = dis.vr();
    int len = dis.length();
    if (TagUtils.isGroupLength(tag)) {
        dis.readValue(dis, attrs);
    } else if (dis.isExcludeBulkData()) {
        dis.readValue(dis, attrs);
    } else {
        gen.writeStartObject(TagUtils.toHexString(tag));
        gen.write("vr", vr.name());
        if (vr == VR.SQ || len == -1) {
            hasItems.addLast(false);
            dis.readValue(dis, attrs);
            if (hasItems.removeLast())
                gen.writeEnd();
        } else if (len > 0) {
            if (dis.isIncludeBulkDataURI()) {
                writeBulkData(dis.createBulkData(dis));
            } else {
                byte[] b = dis.readValue();
                if (tag == Tag.TransferSyntaxUID || tag == Tag.SpecificCharacterSet || TagUtils.isPrivateCreator(tag))
                    attrs.setBytes(tag, vr, b);
                writeValue(vr, b, dis.bigEndian(), attrs.getSpecificCharacterSet(vr), false);
            }
        }
        gen.writeEnd();
    }
}