private Collection getObserverContextItems(String personName) {
Dataset ds = dof.newDataset();
ds.putCS(Tags.RelationshipType, "HAS OBS CONTEXT");
ds.putCS(Tags.ValueType, "CODE");
DcmElement cnSq = ds.putSQ(Tags.ConceptNameCodeSeq);
Dataset cnDS = cnSq.addNewItem();
cnDS.putSH(Tags.CodeValue, "121005");
cnDS.putSH(Tags.CodingSchemeDesignator, "DCM");
cnDS.putLO(Tags.CodeMeaning, "ObserverType");
DcmElement ccSq = ds.putSQ(Tags.ConceptCodeSeq);
Dataset ccDS = ccSq.addNewItem();
ccDS.putSH(Tags.CodeValue, "121006");
ccDS.putSH(Tags.CodingSchemeDesignator, "DCM");
ccDS.putLO(Tags.CodeMeaning, "Person");
Dataset ds1 = dof.newDataset();
ds1.putCS(Tags.RelationshipType, "HAS OBS CONTEXT");
ds1.putCS(Tags.ValueType, "PNAME");
DcmElement cnSq1 = ds1.putSQ(Tags.ConceptNameCodeSeq);
Dataset cnDS1 = cnSq1.addNewItem();
cnDS1.putSH(Tags.CodeValue, "121008");
cnDS1.putSH(Tags.CodingSchemeDesignator, "DCM");
cnDS1.putLO(Tags.CodeMeaning, "Person Observer Name");
ds1.putPN(Tags.PersonName, personName);
ArrayList col = new ArrayList();
col.add(ds);
col.add(ds1);
return col;
}
/**
* Prepares the Dataset representing the search key in C-FIND. As no values are set, the keys
* match to every content in the archive. The user has to specify concret values to limit the
* searchSee PS 3.4 - C.6.2.1.2 Study level.
*
* <p>As the result for C-FIND these keys are filled with the values found in the archive.
*
* @param cfg the configuration properties for this class.
* @throws ParseException if a given properties for the keys was not found.
*/
private void initKeys(ConfigProperties cfg) throws ParseException {
// Remove all keys
keys = dof.newDataset();
// Query/Retrieve Level. PS 3.4 - C.6.2 Study Root SOP Class Group
keys.putCS(Tags.QueryRetrieveLevel, getQueryRetrieveLevel(STUDY_LEVEL));
// UNIQUE STUDY LEVEL KEY FOR THE STUDY. See PS 3.4 - C.6.2.1.2 Study level
keys.putUI(Tags.StudyInstanceUID);
// REQUIRED STUDY LEVEL KEY FOR THE STUDY. See PS 3.4 - C.6.2.1.2 Study level
keys.putDA(Tags.StudyDate);
// Not defined: StudyTime
// Not defined: AccessionNumber
keys.putPN(Tags.PatientName);
keys.putLO(Tags.PatientID);
// Not defined: StudyID
// OPTIONAL STUDY LEVEL KEY FOR THE STUDY. See PS 3.4 - C.6.2.1.2 Study level
keys.putUS(Tags.NumberOfStudyRelatedSeries);
keys.putUS(Tags.NumberOfStudyRelatedInstances);
// mutch more defined...
// Add the keys found in the configuration properties
addQueryKeys(cfg);
}
public void handleNotification(Notification notif, Object handback) {
String spsuid = (String) notif.getUserData();
Dataset pps = DcmObjectFactory.getInstance().newDataset();
try {
Dataset sps;
GPWLManager gpwlmgr = getGPWLManager();
sps = gpwlmgr.getWorklistItem(spsuid);
String ppsiuid = spsuid + ppsuidSuffix;
String status = sps.getString(Tags.GPSPSStatus);
pps.putCS(Tags.GPPPSStatus, status);
pps.putUI(Tags.SOPInstanceUID, ppsiuid);
Date now = new Date();
if ("IN PROGRESS".equals(status)) {
try {
getGPPPSManager().getGPPPS(ppsiuid);
return; // avoid duplicate N_CREATE
} catch (Exception e) {
}
pps.putSH(Tags.PPSID, "PPS" + ppsiuid.hashCode());
pps.putDA(Tags.PPSStartDate, now);
pps.putTM(Tags.PPSStartTime, now);
pps.putDA(Tags.PPSEndDate);
pps.putTM(Tags.PPSEndTime);
for (int i = 0; i < N_CREATE_TYPE2_ATTRS.length; i++) {
pps.putXX(N_CREATE_TYPE2_ATTRS[i]);
}
pps.putAll(sps.subSet(N_CREATE_SPS_ATTRS));
copyCode(
copyWorkitemCode,
sps.getItem(Tags.ScheduledWorkitemCodeSeq),
pps.putSQ(Tags.PerformedWorkitemCodeSeq));
copyCode(
copyStationNameCode,
sps.getItem(Tags.ScheduledStationNameCodeSeq),
pps.putSQ(Tags.PerformedStationNameCodeSeq));
copyCode(
copyStationClassCode,
sps.getItem(Tags.ScheduledStationClassCodeSeq),
pps.putSQ(Tags.PerformedStationClassCodeSeq));
copyCode(
copyStationGeographicLocationCode,
sps.getItem(Tags.ScheduledStationGeographicLocationCodeSeq),
pps.putSQ(Tags.PerformedStationGeographicLocationCodeSeq));
copyCode(
copyProcessingApplicationsCode,
sps.getItem(Tags.ScheduledProcessingApplicationsCodeSeq),
pps.putSQ(Tags.PerformedProcessingApplicationsCodeSeq));
} else if ("COMPLETED".equals(status) || "DISCONTINUED".equals(status)) {
pps.putDA(Tags.PPSEndDate, now);
pps.putTM(Tags.PPSEndTime, now);
pps.putAll(gpwlmgr.getOutputInformation(spsuid));
} else {
return;
}
} catch (Exception e) {
log.error("Failed to access GP-SPS[" + spsuid + "]", e);
return;
}
for (int i = 0; i < destAETs.length; i++) {
PPSOrder order = new PPSOrder(pps, destAETs[i]);
try {
log.info("Scheduling " + order);
jmsDelegate.queue(queueName, order, Message.DEFAULT_PRIORITY, 0L);
} catch (Exception e) {
log.error("Failed to schedule " + order, e);
}
}
}
public Vector cGET(Dataset ds) throws ConnectException, IOException, InterruptedException {
PresContext pc;
List dimseList;
Vector datasetVector;
// An association must be active
if (aassoc == null) {
throw new ConnectException("No Association established");
}
// Test, if Presentation Context for C-MOVE is supported
// API doc: Association.getAcceptedPresContext(String asuid, String tsuid)
if ((pc =
aassoc
.getAssociation()
.getAcceptedPresContext(
UIDs.StudyRootQueryRetrieveInformationModelGET,
UIDs.ExplicitVRLittleEndian))
== null
&& (pc =
aassoc
.getAssociation()
.getAcceptedPresContext(
UIDs.StudyRootQueryRetrieveInformationModelGET,
UIDs.ImplicitVRLittleEndian))
== null) {
throw new ConnectException(
"Association does not support presentation context for StudyRootQueryRetrieveInformationModelMOVE SOP.");
}
// Get the Study Instance UID of the study to mode
String suid = ds.getString(Tags.SOPInstanceUID);
// Prepare info for logging
String patName = ds.getString(Tags.PatientName);
String patID = ds.getString(Tags.PatientID);
String studyDate = ds.getString(Tags.StudyDate);
String prompt =
"Study[" + suid + "] from " + studyDate + " for Patient[" + patID + "]: " + patName;
// log.info("Moving: " + prompt);
// New Cammand Set, see: DICOM Part 7: Message Exchange, 6.3.1 Command Set Structure
Command rqCmd = dof.newCommand();
// API doc: Command.initCMoveRQ(int msgID, String sopClassUID, int priority, String moveDest)
rqCmd.initCGetRSP(assoc.nextMsgID(), UIDs.StudyRootQueryRetrieveInformationModelGET, priority);
Dataset rqDs = dof.newDataset();
rqDs.putCS(Tags.QueryRetrieveLevel, getQueryRetrieveLevel(STUDY_LEVEL));
// Only Unique Key allowed in C-MOVE. PS 3.4 -C.2.2.1 Attribute Types
rqDs.putUI(Tags.SOPInstanceUID, suid);
// API doc: AssociationFactorynewDimse(int pcid, Command cmd, Dataset ds)
// DIMSE (DICOM Message Service Element) ist ein Nachrichtendienst in DICOM
Dimse moveRq = aFact.newDimse(pc.pcid(), rqCmd, rqDs);
// Invoke active association with move request Dimse
FutureRSP future = aassoc.invoke(moveRq);
// Response to the C-MOVE request.
// The result cannot be accessed until it has been set.
Dimse moveRsp = future.get();
Command rspCmd = moveRsp.getCommand();
if (DEBUG) {
StringWriter w = new StringWriter();
w.write("C-FIND RQ Identifier:\n");
keys.dumpDataset(w, null);
log.debug(w.toString());
}
// Invoke active association with find request Dimse
// Response to the C-FIND request.
// The result cannot be accessed until it has been set.
// Get the list of found objects
dimseList = future.listPending();
// >>>> Extract Dataset from Dimse
datasetVector = new Vector();
// If no List of DIMSE objects was generated or it is empty return an empty Vector
if (dimseList == null || dimseList.isEmpty()) {
return datasetVector;
}
// Process all elements
for (int i = 0; i < dimseList.size(); i++) {
datasetVector.addElement(((Dimse) dimseList.get(i)).getDataset());
if (((Dimse) dimseList.get(i)).getDataset() == null)
System.out.println(" Dataset created succesffullyu ");
}
// PS 3.7 - 9.3.4 C-MOVE PROTOCOL, 9.3.4.2 C-MOVE-RSP
int status = rspCmd.getStatus();
switch (status) {
case 0x0000:
// log.info("Moved: " + prompt);
break;
case 0xB000:
log.error("One or more failures during move of " + prompt);
break;
default:
log.error("Failed to move " + prompt + "\n\terror tstatus: " + Integer.toHexString(status));
break;
}
System.out.println("The move sise is : " + datasetVector.size());
return datasetVector;
}
/**
* Convert an image to RGB.
*
* @param inFile the file to convert.
* @param outFile the output file, which may be same as inFile.
* @return the static status result
*/
public static AnonymizerStatus convert(File inFile, File outFile) {
long fileLength = inFile.length();
logger.debug("Entering DICOMPaletteImageConverter.convert");
logger.debug("File length = " + fileLength);
BufferedInputStream in = null;
BufferedOutputStream out = null;
File tempFile = null;
byte[] buffer = new byte[4096];
try {
// Check that this is a known format.
in = new BufferedInputStream(new FileInputStream(inFile));
DcmParser parser = pFact.newDcmParser(in);
FileFormat fileFormat = parser.detectFileFormat();
if (fileFormat == null) {
throw new IOException("Unrecognized file format: " + inFile);
}
// Get the dataset (excluding pixels) and leave the input stream open
Dataset dataset = oFact.newDataset();
parser.setDcmHandler(dataset.getDcmHandler());
parser.parseDcmFile(fileFormat, Tags.PixelData);
// Make sure this is an image
if (parser.getReadTag() != Tags.PixelData) {
close(in);
return AnonymizerStatus.SKIP(inFile, "Not an image");
}
// Get the required parameters and make sure they are okay
int numberOfFrames = getInt(dataset, Tags.NumberOfFrames, 1);
int rows = getInt(dataset, Tags.Rows, 0);
int columns = getInt(dataset, Tags.Columns, 0);
String photometricInterpretation = getString(dataset, Tags.PhotometricInterpretation, "");
if ((rows == 0) || (columns == 0)) {
close(in);
return AnonymizerStatus.SKIP(inFile, "Unable to get the rows and columns");
}
if (!photometricInterpretation.equals("PALETTE COLOR")) {
close(in);
return AnonymizerStatus.SKIP(
inFile, "Unsupported PhotometricInterpretation: " + photometricInterpretation);
}
if (parser.getReadTag() != Tags.PixelData) {
close(in);
return AnonymizerStatus.SKIP(inFile, "No pixels");
}
// Get the encoding and set the parameters
DcmDecodeParam fileParam = parser.getDcmDecodeParam();
String fileEncodingUID = UIDs.ImplicitVRLittleEndian;
FileMetaInfo fmi = dataset.getFileMetaInfo();
if (fmi != null) fileEncodingUID = fmi.getTransferSyntaxUID();
boolean isBigEndian = fileEncodingUID.equals(UIDs.ExplicitVRBigEndian);
String encodingUID = UIDs.ExplicitVRLittleEndian;
DcmEncodeParam encoding = (DcmEncodeParam) DcmDecodeParam.valueOf(encodingUID);
boolean swap = (fileParam.byteOrder != encoding.byteOrder);
if (encoding.encapsulated) {
logger.debug("Encapsulated pixel data found");
close(in);
return AnonymizerStatus.SKIP(inFile, "Encapsulated pixel data not supported");
}
// Get the LUTs
LUT red =
new LUT(
dataset.getInts(Tags.RedPaletteColorLUTDescriptor),
dataset.getInts(Tags.RedPaletteColorLUTData));
LUT green =
new LUT(
dataset.getInts(Tags.GreenPaletteColorLUTDescriptor),
dataset.getInts(Tags.GreenPaletteColorLUTData));
LUT blue =
new LUT(
dataset.getInts(Tags.BluePaletteColorLUTDescriptor),
dataset.getInts(Tags.BluePaletteColorLUTData));
// Set the PlanarConfiguration to 0
dataset.putUS(Tags.PlanarConfiguration, 0);
// Set the PhotometricInterpretation to RGB
dataset.putCS(Tags.PhotometricInterpretation, "RGB");
// Set the pixel parameters
dataset.putUS(Tags.SamplesPerPixel, 3);
dataset.putUS(Tags.BitsAllocated, 8);
dataset.putUS(Tags.BitsStored, 8);
dataset.putUS(Tags.HighBit, 7);
// Remove the lookup tables and their descriptors
dataset.remove(Tags.RedPaletteColorLUTDescriptor);
dataset.remove(Tags.GreenPaletteColorLUTDescriptor);
dataset.remove(Tags.BluePaletteColorLUTDescriptor);
dataset.remove(Tags.RedPaletteColorLUTData);
dataset.remove(Tags.GreenPaletteColorLUTData);
dataset.remove(Tags.BluePaletteColorLUTData);
// Save the dataset to a temporary file, and rename at the end.
File tempDir = outFile.getParentFile();
tempFile = File.createTempFile("DCMtemp-", ".anon", tempDir);
out = new BufferedOutputStream(new FileOutputStream(tempFile));
// Create and write the metainfo for the encoding we are using
fmi = oFact.newFileMetaInfo(dataset, encodingUID);
dataset.setFileMetaInfo(fmi);
fmi.write(out);
// Write the dataset as far as was parsed
dataset.writeDataset(out, encoding);
// Process the pixels
int nPixels = numberOfFrames * rows * columns;
int nPixelBytes = nPixels * 3 /*samplesPerPixel*/;
int pad = nPixelBytes & 1;
dataset.writeHeader(out, encoding, parser.getReadTag(), VRs.OB, nPixelBytes + pad);
int pd;
int b1, b2;
int bytesPerFrame = rows * columns * 2;
byte[] frameBytes = new byte[bytesPerFrame];
for (int frame = 0; frame < numberOfFrames; frame++) {
if (in.read(frameBytes, 0, frameBytes.length) != bytesPerFrame)
throw new Exception("End of File");
for (int p = 0; p < bytesPerFrame; ) {
b1 = frameBytes[p++];
b2 = frameBytes[p++];
if (!swap) {
pd = ((b2 & 0xff) << 8) | (b1 & 0xff);
} else {
pd = ((b1 & 0xff) << 8) | (b2 & 0xff);
}
out.write(red.get(pd));
out.write(green.get(pd));
out.write(blue.get(pd));
}
}
if (pad != 0) out.write(0);
logger.debug("Finished writing the pixels");
// Skip everything after the pixels
out.flush();
out.close();
in.close();
outFile.delete();
tempFile.renameTo(outFile);
return AnonymizerStatus.OK(outFile, "");
} catch (Exception e) {
logger.debug("Exception while processing image.", e);
// Close the input stream if it actually got opened.
close(in);
// Close the output stream if it actually got opened,
// and delete the tempFile in case it is still there.
try {
if (out != null) {
out.close();
tempFile.delete();
}
} catch (Exception ex) {
logger.warn("Unable to close the output stream.");
}
// Quarantine the object
return AnonymizerStatus.QUARANTINE(inFile, e.getMessage());
}
}
