@Override
public void readValue(Object data, Tagable tagabale) {
if (data instanceof MacroSeqData) {
MacroSeqData macro = (MacroSeqData) data;
Object val = getValue(macro.getAttributes());
if (val instanceof Sequence) {
Sequence seq = (Sequence) val;
if (!seq.isEmpty()) {
val = seq.get(0);
}
}
if (val instanceof Attributes) {
Attributes dataset = (Attributes) val;
Predicate<? super Attributes> predicate = macro.getApplicable();
if (predicate == null || predicate.test(dataset)) {
for (TagW tag : macro.getTags()) {
if (tag != null) {
tag.readValue(dataset, tagabale);
}
}
}
}
}
}
private Attributes sopRef(StoreContext ctx) {
StoreSession session = ctx.getStoreSession();
Attributes attrs = ctx.getAttributes();
Attributes sopRef = new Attributes(5);
String cuid = attrs.getString(Tag.SOPClassUID);
String iuid = attrs.getString(Tag.SOPInstanceUID);
String series_iuid = attrs.getString(Tag.SeriesInstanceUID);
String study_iuid = attrs.getString(Tag.StudyInstanceUID);
sopRef.setString(Tag.ReferencedSOPClassUID, VR.UI, cuid);
sopRef.setString(Tag.ReferencedSOPInstanceUID, VR.UI, iuid);
sopRef.setString(
Tag.RetrieveURL,
VR.UR,
wadoURL + study_iuid + "/series/" + series_iuid + "/instances/" + iuid);
Attributes coercedAttrs = ctx.getCoercedOriginalAttributes();
if (!coercedAttrs.isEmpty()) {
sopRef.setInt(Tag.WarningReason, VR.US, org.dcm4che3.net.Status.CoercionOfDataElements);
Attributes item = new Attributes(4);
Sequence origAttrsSeq = sopRef.ensureSequence(Tag.OriginalAttributesSequence, 1);
origAttrsSeq.add(item);
item.setDate(Tag.AttributeModificationDateTime, VR.DT, new Date());
item.setString(Tag.ModifyingSystem, VR.LO, session.getStoreParam().getModifyingSystem());
item.setString(Tag.SourceOfPreviousValues, VR.LO, session.getRemoteAET());
item.newSequence(Tag.ModifiedAttributesSequence, 1).add(coercedAttrs);
}
return sopRef;
}
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);
}
private Attributes nestedKeys(int[] tags) {
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);
}
return item;
}
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) return voiLUT;
for (int refFrame : refFrames) if (refFrame == frame) return voiLUT;
}
}
}
return null;
}
private void storageFailed(String iuid, String cuid, int failureReason) {
Attributes sopRef = new Attributes(3);
sopRef.setString(Tag.ReferencedSOPClassUID, VR.UI, cuid);
sopRef.setString(Tag.ReferencedSOPInstanceUID, VR.UI, iuid);
sopRef.setInt(Tag.FailureReason, VR.US, failureReason);
if (failedSOPSequence == null)
failedSOPSequence = response.newSequence(Tag.FailedSOPSequence, 10);
failedSOPSequence.add(sopRef);
}
private Response buildResponse() {
// if (sopSequence.isEmpty())
// throw new WebApplicationException(Status.CONFLICT);
return Response.status(
sopSequence.isEmpty()
? Status.CONFLICT
: failedSOPSequence == null ? Status.OK : Status.ACCEPTED)
.entity(
new StreamingOutput() {
@Override
public void write(OutputStream out) throws IOException, WebApplicationException {
try {
SAXTransformer.getSAXWriter(new StreamResult(out)).write(response);
} catch (Exception e) {
throw new WebApplicationException(e);
}
}
})
.type(MediaTypes.APPLICATION_DICOM_XML_TYPE)
.build();
}
private void storeMetadataAndBulkdata(StoreSession session, MetaDataPathTSTuple part) {
Attributes ds = null;
if (creatorType == CreatorType.JSON_BULKDATA) {
try {
ds = parseJSON(part.getPath().toFile().getPath());
} catch (Exception e) {
storageFailed(NOT_PARSEABLE_IUID, NOT_PARSEABLE_CUID, METADATA_NOT_PARSEABLE);
return;
}
} else {
try {
ds = SAXReader.parse(part.getPath().toUri().toString());
} catch (Exception e) {
storageFailed(NOT_PARSEABLE_IUID, NOT_PARSEABLE_CUID, METADATA_NOT_PARSEABLE);
return;
}
}
String iuid = ds.getString(Tag.SOPInstanceUID);
String cuid = ds.getString(Tag.SOPClassUID);
Attributes fmi = ds.createFileMetaInformation(part.getTransferSyntax());
if (!resolveBulkdata(session, fmi, ds)) {
storageFailed(iuid, cuid, MISSING_BULKDATA);
return;
}
try {
checkStudyInstanceUID(ds.getString(Tag.StudyInstanceUID));
checkTransferCapability(cuid, fmi.getString(Tag.TransferSyntaxUID));
StoreContext context = storeService.createStoreContext(session);
storeService.writeSpoolFile(context, fmi, ds);
storeService.store(context);
sopSequence.add(sopRef(context));
} catch (DicomServiceException e) {
storageFailed(iuid, cuid, e.getStatus());
}
}
private void storeDicomObject(StoreSession session, InputStream in) throws DicomServiceException {
StoreContext context;
try {
context = storeService.createStoreContext(session);
storeService.writeSpoolFile(context, null, in);
storeService.parseSpoolFile(context);
} catch (DicomServiceException e) {
if (e.getStatus() == StoreService.DATA_SET_NOT_PARSEABLE) {
storageFailed(NOT_PARSEABLE_IUID, NOT_PARSEABLE_CUID, METADATA_NOT_PARSEABLE);
return;
}
throw e;
}
Attributes attrs = context.getAttributes();
try {
checkStudyInstanceUID(attrs.getString(Tag.StudyInstanceUID));
checkTransferCapability(attrs.getString(Tag.SOPClassUID), context.getTransferSyntax());
storeService.store(context);
sopSequence.add(sopRef(context));
} catch (DicomServiceException e) {
storageFailed(
attrs.getString(Tag.SOPInstanceUID), attrs.getString(Tag.SOPClassUID), e.getStatus());
}
}
@Test
public void testPart10Deflated() throws Exception {
Attributes attrs = readFromResource("report_dfl", IncludeBulkData.YES);
Sequence seq = attrs.getSequence(null, Tag.ContentSequence);
assertEquals(5, seq.size());
}
@Test
public void testPart10ExplicitVR() throws Exception {
Attributes attrs = readFromResource("DICOMDIR", IncludeBulkData.YES);
Sequence seq = attrs.getSequence(null, Tag.DirectoryRecordSequence);
assertEquals(44, seq.size());
}