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

Example 1 with Attributes

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

the class GatewaySetUpService method addDestinationNode.

private void addDestinationNode(List<ForwardDestination> dstList, ForwardDicomNode fwdSrcNode, DestinationEntity dstNode) {
    try {
        List<AttributeEditor> editors = new ArrayList<>();
        if (!dstNode.getCondition().isEmpty()) {
            editors.add(new ConditionEditor(dstNode.getCondition()));
        }
        final boolean filterBySOPClassesEnable = dstNode.isFilterBySOPClasses();
        if (filterBySOPClassesEnable) {
            editors.add(new FilterEditor(dstNode.getSOPClassUIDEntityFilters()));
        }
        final List<KheopsAlbumsEntity> kheopsAlbumEntities = dstNode.getKheopsAlbumEntities();
        SwitchingAlbum switchingAlbum = new SwitchingAlbum();
        if (kheopsAlbumEntities != null && !kheopsAlbumEntities.isEmpty()) {
            editors.add((Attributes dcm, AttributeEditorContext context) -> {
                kheopsAlbumEntities.forEach(kheopsAlbums -> {
                    switchingAlbum.apply(dstNode, kheopsAlbums, dcm);
                });
            });
        }
        StreamRegistryEditor streamRegistryEditor = new StreamRegistryEditor();
        editors.add(streamRegistryEditor);
        boolean deidentificationEnable = dstNode.isDesidentification();
        boolean profileDefined = dstNode.getProjectEntity() != null && dstNode.getProjectEntity().getProfileEntity() != null;
        if (deidentificationEnable && profileDefined) {
            // TODO add an option in destination model
            editors.add(new DeIdentifyEditor(dstNode));
        }
        DicomProgress progress = new DicomProgress();
        if (dstNode.isActivate()) {
            if (dstNode.getDestinationType() == DestinationType.stow) {
                // parse headers to hashmap
                HashMap<String, String> map = new HashMap<>();
                String headers = dstNode.getHeaders();
                Document doc = Jsoup.parse(headers);
                String key = doc.getElementsByTag("key").text();
                String value = doc.getElementsByTag("value").text();
                if (StringUtil.hasText(key)) {
                    map.put(key, value);
                }
                WebForwardDestination fwd = new WebForwardDestination(dstNode.getId(), fwdSrcNode, dstNode.getUrl(), map, progress, editors, dstNode.getTransferSyntax(), dstNode.isTranscodeOnlyUncompressed());
                if (kheopsAlbumEntities != null && !kheopsAlbumEntities.isEmpty()) {
                    progress.addProgressListener((DicomProgress dicomProgress) -> {
                        Attributes dcm = dicomProgress.getAttributes();
                        kheopsAlbumEntities.forEach(kheopsAlbums -> {
                            switchingAlbum.applyAfterTransfer(kheopsAlbums, dcm);
                        });
                    });
                }
                dstList.add(fwd);
            } else {
                DicomNode destinationNode = new DicomNode(dstNode.getAeTitle(), dstNode.getHostname(), dstNode.getPort());
                DicomForwardDestination dest = new DicomForwardDestination(dstNode.getId(), getDefaultAdvancedParameters(), fwdSrcNode, destinationNode, dstNode.getUseaetdest(), progress, editors, dstNode.getTransferSyntax(), dstNode.isTranscodeOnlyUncompressed());
                dstList.add(dest);
            }
        }
    } catch (IOException e) {
        LOGGER.error("Cannot build ForwardDestination", e);
    }
}

Example 2 with Attributes

use of org.dcm4che3.data.Attributes 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 3 with Attributes

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

the class Profile method apply.

public void apply(Attributes dcm, DestinationEntity destinationEntity, ProfileEntity profileEntity, AttributeEditorContext context) {
    final String SOPInstanceUID = dcm.getString(Tag.SOPInstanceUID);
    final String SeriesInstanceUID = dcm.getString(Tag.SeriesInstanceUID);
    final String IssuerOfPatientID = dcm.getString(Tag.IssuerOfPatientID);
    final String PatientID = dcm.getString(Tag.PatientID);
    final HMAC hmac = generateHMAC(destinationEntity, PatientID);
    MDC.put("SOPInstanceUID", SOPInstanceUID);
    MDC.put("SeriesInstanceUID", SeriesInstanceUID);
    MDC.put("issuerOfPatientID", IssuerOfPatientID);
    MDC.put("PatientID", PatientID);
    String pseudonymValue = this.pseudonym.generatePseudonym(destinationEntity, dcm);
    String profilesCodeName = profiles.stream().map(ProfileItem::getCodeName).collect(Collectors.joining("-"));
    BigInteger patientValue = generatePatientID(pseudonymValue, hmac);
    String newPatientID = patientValue.toString(16).toUpperCase();
    Attributes dcmCopy = new Attributes(dcm);
    // Apply clean pixel data
    applyCleanPixelData(dcmCopy, context, profileEntity);
    // Apply clean recognizable visual features option
    applyDefacing(dcmCopy, context);
    applyAction(dcm, dcmCopy, hmac, null, null, context);
    // Set tags by default
    AttributesByDefault.setPatientModule(dcm, newPatientID, pseudonymValue, destinationEntity.getProjectEntity());
    AttributesByDefault.setSOPCommonModule(dcm);
    AttributesByDefault.setClinicalTrialAttributes(dcm, destinationEntity.getProjectEntity(), pseudonymValue);
    final Marker clincalMarker = MarkerFactory.getMarker("CLINICAL");
    MDC.put("DeidentifySOPInstanceUID", dcm.getString(Tag.SOPInstanceUID));
    MDC.put("DeidentifySeriesInstanceUID", dcm.getString(Tag.SeriesInstanceUID));
    MDC.put("ProjectName", destinationEntity.getProjectEntity().getName());
    MDC.put("ProfileName", profileEntity.getName());
    MDC.put("ProfileCodenames", profilesCodeName);
    LOGGER.info(clincalMarker, "");
    MDC.clear();
}

Example 4 with Attributes

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

the class Profile method applyCleanPixelData.

public void applyCleanPixelData(Attributes dcmCopy, AttributeEditorContext context, ProfileEntity profileEntity) {
    Object pix = dcmCopy.getValue(Tag.PixelData);
    if ((pix instanceof BulkData || pix instanceof Fragments) && !profileEntity.getMaskEntities().isEmpty() && profiles.stream().anyMatch(p -> p instanceof CleanPixelData)) {
        String sopClassUID = dcmCopy.getString(Tag.SOPClassUID);
        if (!StringUtil.hasText(sopClassUID)) {
            throw new IllegalStateException("DICOM Object does not contain sopClassUID");
        }
        String scuPattern = sopClassUID + ".";
        MaskArea mask = getMask(dcmCopy.getString(Tag.StationName));
        // BurnedInAnnotation
        if (isCleanPixelAllowedDependingImageType(dcmCopy, sopClassUID, scuPattern) && evaluateConditionCleanPixelData(dcmCopy)) {
            context.setMaskArea(mask);
            if (mask == null) {
                throw new IllegalStateException("Clean pixel is not applied: mask not defined in station name");
            }
        } else {
            context.setMaskArea(null);
        }
    }
}

Example 5 with Attributes

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

the class MetadataDICOMObject method getValueRec.

private static String getValueRec(Attributes dcm, int tag) {
    String tagValue = dcm.getString(tag);
    Attributes dcmParent = dcm.getParent();
    if (dcmParent != null && tagValue == null) {
        return getValueRec(dcmParent, tag);
    }
    return tagValue;
}