private void echo(ActiveAssociation aa, int nrOfTests) throws Exception {
AssociationFactory aFact = AssociationFactory.getInstance();
DcmObjectFactory oFact = DcmObjectFactory.getInstance();
for (int i = 0; i < nrOfTests; i++) {
aa.invoke(aFact.newDimse(PCID_ECHO, oFact.newCommand().initCEchoRQ(i)), null);
}
}
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);
}
private Map string2Codes(String codes, String defaultDesign) {
StringTokenizer st = new StringTokenizer(codes, ",");
Map map = new HashMap();
int nrOfTokens;
StringTokenizer stCode;
Dataset ds;
String codeValue;
while (st.hasMoreTokens()) {
stCode = new StringTokenizer(st.nextToken(), "^");
nrOfTokens = stCode.countTokens();
if (nrOfTokens < 2) {
throw new IllegalArgumentException(
"Wrong format of human performer configuration! (<codeValue>[^<designator>]^<meaning>)");
}
ds = dof.newDataset();
codeValue = stCode.nextToken();
ds.putSH(Tags.CodeValue, codeValue);
if (nrOfTokens > 2) {
ds.putSH(Tags.CodingSchemeDesignator, stCode.nextToken());
} else if (defaultDesign != null) {
ds.putSH(Tags.CodingSchemeDesignator, defaultDesign);
}
ds.putLO(Tags.CodeMeaning, stCode.nextToken());
map.put(codeValue, ds);
}
return map;
}
/**
* Sets the Dataset representing the query keys in C-FIND. The user can specify concret values to
* limit the search.
*
* <p>Wildcards '*','?', '-' and '\' are allowed as element-values (see PS 3.4 - C.2.2.2 Attribute
* Matching). If an key attribute is defined, but has an empty value, it matches every value at
* the storage side.
*
* <p>At a minimum the key "QueryRetrieveLevel" must be set ("STUDY", "SERIES" or "IMAGE"). See PS
* 3.4 - C.6.2 Study Root SOP Class Group
*
* <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.
*/
public void setQueryKeys(ConfigProperties cfg) throws ParseException {
// Remove all keys
keys = dof.newDataset();
// Add the keys found in the configuration properties
addQueryKeys(cfg);
}
/**
* @param xdsiModel
* @return
*/
private Dataset getRootInfo(XDSIModel xdsiModel) {
Dataset rootInfo = DcmObjectFactory.getInstance().newDataset();
DcmElement sq = rootInfo.putSQ(Tags.ConceptNameCodeSeq);
Dataset item = sq.addNewItem();
CodeItem selectedDocTitle = xdsiModel.selectedDocTitle();
item.putSH(Tags.CodeValue, selectedDocTitle.getCodeValue());
item.putSH(Tags.CodingSchemeDesignator, selectedDocTitle.getCodeDesignator());
item.putLO(Tags.CodeMeaning, selectedDocTitle.getCodeMeaning());
return rootInfo;
}
private PersonName newPersonName(String pname) {
try {
return DcmObjectFactory.getInstance().newPersonName(pname);
} catch (IllegalArgumentException e) {
LOG.warn(
"Cannot generate Soundex code for Illegal Person Name: "
+ pname
+ " - treat as unknown.");
return null;
}
}
public static boolean equalsPixelData(File f1, File f2) throws IOException {
InputStream in1 = new BufferedInputStream(new FileInputStream(f1));
try {
InputStream in2 = new BufferedInputStream(new FileInputStream(f2));
try {
Dataset attrs = DcmObjectFactory.getInstance().newDataset();
DcmParserFactory pf = DcmParserFactory.getInstance();
DcmParser p1 = pf.newDcmParser(in1);
DcmParser p2 = pf.newDcmParser(in2);
p1.setDcmHandler(attrs.getDcmHandler());
p1.parseDcmFile(FileFormat.DICOM_FILE, Tags.PixelData);
p2.parseDcmFile(FileFormat.DICOM_FILE, Tags.PixelData);
int samples = attrs.getInt(Tags.SamplesPerPixel, 1);
int frames = attrs.getInt(Tags.NumberOfFrames, 1);
int rows = attrs.getInt(Tags.Rows, 1);
int columns = attrs.getInt(Tags.Columns, 1);
int bitsAlloc = attrs.getInt(Tags.BitsAllocated, 8);
int bitsStored = attrs.getInt(Tags.BitsStored, bitsAlloc);
int frameLength = rows * columns * samples * bitsAlloc / 8;
int pixelDataLength = frameLength * frames;
if (pixelDataLength > p1.getReadLength() || pixelDataLength > p2.getReadLength()) {
return false;
}
byte[] b1 = new byte[BUFFER_SIZE];
byte[] b2 = new byte[BUFFER_SIZE];
int[] mask = {0xff, 0xff};
int len, len2;
if (bitsAlloc == 16 && bitsStored < 16) {
mask[p1.getDcmDecodeParam().byteOrder == ByteOrder.LITTLE_ENDIAN ? 1 : 0] =
0xff >>> (16 - bitsStored);
}
int pos = 0;
while (pos < pixelDataLength) {
len = in1.read(b1, 0, Math.min(pixelDataLength - pos, BUFFER_SIZE));
if (len < 0) // EOF
return false;
int off = 0;
while (off < len) {
off += len2 = in2.read(b2, off, len - off);
if (len2 < 0) // EOF
return false;
}
for (int i = 0; i < len; i++, pos++)
if (((b1[i] - b2[i]) & mask[pos & 1]) != 0) return false;
}
return true;
} finally {
in2.close();
}
} finally {
in1.close();
}
}
/**
* Implements the ECHO service. The C-ECHO service is invoked by a DIMSE-service-user to verify
* end-to-end communications with a peer DIMSE-service-user. See PS 3.7 - 9.1.5 C-ECHO SERVICE
*
* @exception ConnectException
* @exception InterruptedException
* @exception IOException
*/
public long cECHO() throws ConnectException, InterruptedException, IOException {
PresContext pc;
long t1 = System.currentTimeMillis();
// An association must be active
if (aassoc == null) {
throw new ConnectException("No Association established");
}
// Test, if Presentation Context for C-ECHO is supported
// API doc: Association.getAcceptedPresContext(String asuid, String tsuid)
if ((pc =
aassoc
.getAssociation()
.getAcceptedPresContext(UIDs.Verification, UIDs.ImplicitVRLittleEndian))
== null) {
throw new ConnectException(
"Association does not support presentation context: Verification SOP/ImplicitVRLittleEndian.");
}
// New Cammand Set, see: DICOM Part 7: Message Exchange, 6.3.1 Command Set Structure
Command cEchoRQ = oFact.newCommand();
// API doc: Command.initCEchoRQ(int msgID)
cEchoRQ.initCEchoRQ(1);
// API doc: AssociationFactorynewDimse(int pcid, Command cmd)
// DIMSE (DICOM Message Service Element) ist ein Nachrichtendienst in DICOM
Dimse echoRq = aFact.newDimse(pc.pcid(), cEchoRQ);
// PS 3.7 - 9.3.5 C-ECHO PROTOCOL, 9.3.5.2 C-ECHO-RSP
// Always returns SUCESS result code.
// Invoke active association with echo request Dimse
FutureRSP future = aassoc.invoke(echoRq);
// Response to the C-ECHO request.
// The result cannot be accessed until it has been set.
Dimse echoRsp = future.get();
Command rspCmd = echoRsp.getCommand();
// PS 3.7 - 9.3.5 C-MOVE PROTOCOL, 9.3.5.2 C-ECHO-RSP
int status = rspCmd.getStatus();
switch (status) {
case 0x0000:
// Success
break;
default:
log.error("C-ECHO failed: " + Integer.toHexString(status));
break;
}
return System.currentTimeMillis() - t1;
}
void sendPPS(boolean create, Dataset pps, String aet) throws Exception {
ActiveAssociation aa = openAssociation(aet, UIDs.GeneralPurposePerformedProcedureStepSOPClass);
try {
Association a = aa.getAssociation();
DcmObjectFactory dof = DcmObjectFactory.getInstance();
Command cmdRq = dof.newCommand();
final String iuid = pps.getString(Tags.SOPInstanceUID);
if (create) {
cmdRq.initNCreateRQ(a.nextMsgID(), UIDs.GeneralPurposePerformedProcedureStepSOPClass, iuid);
} else {
cmdRq.initNSetRQ(a.nextMsgID(), UIDs.GeneralPurposePerformedProcedureStepSOPClass, iuid);
}
Dimse dimseRq =
AssociationFactory.getInstance().newDimse(PCID_GPPPS, cmdRq, pps.exclude(SOP_IUID));
if (log.isDebugEnabled()) {
log.debug("GP-PPS Attributes:");
log.debug(pps);
}
final Dimse dimseRsp = aa.invoke(dimseRq).get();
final Command cmdRsp = dimseRsp.getCommand();
final int status = cmdRsp.getStatus();
switch (status) {
case 0x0000:
break;
case 0x0116:
log.warn(
"Received Warning Status 116H (=Attribute Value Out of Range) from remote AE " + aet);
break;
default:
throw new DcmServiceException(status, cmdRsp.getString(Tags.ErrorComment));
}
} finally {
try {
aa.release(true);
} catch (Exception e) {
log.warn("Failed to release " + aa.getAssociation());
}
}
}
private Dataset loadDataset(File file) throws IOException {
BufferedInputStream bis = new BufferedInputStream(new FileInputStream(file));
Dataset ds = factory.newDataset();
try {
ds.readFile(bis, null, -1);
} finally {
try {
bis.close();
} catch (IOException ignore) {
}
}
if (log.isDebugEnabled()) log.debug("Dataset for file " + file + " :" + ds);
return ds;
}
/**
* Imports a DICOM file.
*
* <p>The FileDTO object refers to an existing DICOM file (This method does NOT check this file!)
* and the Dataset object holds the meta data for database.
*
* <p>
*
* @param fileDTO Refers the DICOM file.
* @param ds Dataset with metadata for database.
* @param last last file to import
*/
public void importFile(FileDTO fileDTO, Dataset ds, String prevseriuid, boolean last)
throws Exception {
Storage store = getStorage();
String seriud = ds.getString(Tags.SeriesInstanceUID);
if (prevseriuid != null && !prevseriuid.equals(seriud)) {
SeriesStored seriesStored = store.makeSeriesStored(prevseriuid);
if (seriesStored != null) {
log.debug("Send SeriesStoredNotification - series changed");
scp.doAfterSeriesIsStored(store, null, seriesStored);
}
}
String cuid = ds.getString(Tags.SOPClassUID);
String iuid = ds.getString(Tags.SOPInstanceUID);
FileMetaInfo fmi =
DcmObjectFactory.getInstance().newFileMetaInfo(cuid, iuid, fileDTO.getFileTsuid());
ds.setFileMetaInfo(fmi);
String fsPath = fileDTO.getDirectoryPath();
String filePath = fileDTO.getFilePath();
File f = FileUtils.toFile(fsPath, filePath);
// Modified by [email protected] on 01.09.2009
// In case the file is not stored in file system but somewhere else
// scp.updateDB(store, ds, fileDTO.getFileSystemPk(), filePath, f.length(),
// fileDTO.getFileMd5(), true);
scp.updateDB(
store,
ds,
fileDTO.getFileSystemPk(),
filePath,
fileDTO.getFileSize(),
fileDTO.getFileMd5(),
true);
if (last) {
SeriesStored seriesStored = store.makeSeriesStored(seriud);
if (seriesStored != null) {
scp.doAfterSeriesIsStored(store, null, seriesStored);
}
}
}
private Dataset getStudyMgtDataset(StudyLocal study, Map mapSeries) {
Dataset ds = dof.newDataset();
ds.putUI(Tags.StudyInstanceUID, study.getStudyIuid());
ds.putOB(PrivateTags.StudyPk, Convert.toBytes(study.getPk().longValue()));
ds.putSH(Tags.AccessionNumber, study.getAccessionNumber());
ds.putLO(Tags.PatientID, study.getPatient().getPatientId());
ds.putLO(Tags.IssuerOfPatientID, study.getPatient().getIssuerOfPatientId());
ds.putPN(Tags.PatientName, study.getPatient().getPatientName());
log.debug("getStudyMgtDataset: studyIUID:" + study.getStudyIuid());
DcmElement refSeriesSeq = ds.putSQ(Tags.RefSeriesSeq);
Iterator iter =
(mapSeries == null) ? study.getSeries().iterator() : mapSeries.keySet().iterator();
while (iter.hasNext()) {
SeriesLocal sl = (SeriesLocal) iter.next();
Dataset dsSer = refSeriesSeq.addNewItem();
dsSer.putUI(Tags.SeriesInstanceUID, sl.getSeriesIuid());
Collection instances =
(mapSeries == null) ? sl.getInstances() : (Collection) mapSeries.get(sl);
Iterator iter2 = instances.iterator();
DcmElement refSopSeq = null;
if (iter2.hasNext()) refSopSeq = dsSer.putSQ(Tags.RefSOPSeq);
while (iter2.hasNext()) {
InstanceLocal il = (InstanceLocal) iter2.next();
Dataset dsInst = refSopSeq.addNewItem();
dsInst.putUI(Tags.RefSOPClassUID, il.getSopCuid());
dsInst.putUI(Tags.RefSOPInstanceUID, il.getSopIuid());
dsInst.putAE(Tags.RetrieveAET, il.getRetrieveAETs());
}
}
if (log.isDebugEnabled()) {
log.debug("return StgMgtDataset:");
log.debug(ds);
}
return ds;
}
/** * @author [email protected] * @version $Revision: 3345 $ $Date: 2007-05-18 10:53:26 +0200 (Fr, 18. Mai 2007) $ * @since 05.04.2005 */ public class GPWLFeedService extends ServiceMBeanSupport { private static final int[] PAT_ATTR_TAGS = { Tags.PatientName, Tags.PatientID, Tags.PatientBirthDate, Tags.PatientSex, }; private Map humanPerformer = null; private List templates = null; private File templatePath = null; private static DcmObjectFactory dof = DcmObjectFactory.getInstance(); /** @return Returns the physicians. */ public String getHumanPerformer() { return codes2String(humanPerformer); } /** @param performer The human performer(s) to set. */ public void setHumanPerformer(String performer) { this.humanPerformer = string2Codes(performer, "DCM4CHEE"); } /** @return Returns the configURL. */ public String getTemplatePath() { return templatePath.getPath(); } /** * @param configURL The configURL to set. * @throws MalformedURLException */ public void setTemplatePath(String path) throws MalformedURLException { templatePath = new File(path.replace('/', File.separatorChar)); } private String codes2String(Map codes) { if (codes == null || codes.isEmpty()) return ""; StringBuffer sb = new StringBuffer(); Dataset ds; String design; for (Iterator iter = codes.values().iterator(); iter.hasNext(); ) { ds = (Dataset) iter.next(); design = ds.getString(Tags.CodingSchemeDesignator); sb.append(ds.getString(Tags.CodeValue)).append("^"); if (design != null) sb.append(design).append("^"); sb.append(ds.getString(Tags.CodeMeaning)).append(","); } return sb.substring(0, sb.length() - 1); } private Map string2Codes(String codes, String defaultDesign) { StringTokenizer st = new StringTokenizer(codes, ","); Map map = new HashMap(); int nrOfTokens; StringTokenizer stCode; Dataset ds; String codeValue; while (st.hasMoreTokens()) { stCode = new StringTokenizer(st.nextToken(), "^"); nrOfTokens = stCode.countTokens(); if (nrOfTokens < 2) { throw new IllegalArgumentException( "Wrong format of human performer configuration! (<codeValue>[^<designator>]^<meaning>)"); } ds = dof.newDataset(); codeValue = stCode.nextToken(); ds.putSH(Tags.CodeValue, codeValue); if (nrOfTokens > 2) { ds.putSH(Tags.CodingSchemeDesignator, stCode.nextToken()); } else if (defaultDesign != null) { ds.putSH(Tags.CodingSchemeDesignator, defaultDesign); } ds.putLO(Tags.CodeMeaning, stCode.nextToken()); map.put(codeValue, ds); } return map; } public List listTemplates() { if (templates == null) { File tmplPath = FileUtils.resolve(templatePath); File[] files = tmplPath.listFiles(); templates = new ArrayList(); String fn; for (int i = 0; i < files.length; i++) { fn = files[i].getName(); if (fn.endsWith(".xml")) { templates.add(fn.substring(0, fn.length() - 4)); } } } log.info("Template List:" + templates); return templates; } public void clearTemplateList() { templates = null; } public void addWorklistItem( Long studyPk, String templateFile, String humanPerformerCode, Long scheduleDate) throws Exception { String uri = FileUtils.resolve(new File(templatePath, templateFile + ".xml")).toURI().toString(); if (log.isDebugEnabled()) log.debug("load template file: " + uri); Dataset ds = DatasetUtils.fromXML(new InputSource(uri)); ContentManager cm = getContentManager(); // patient Dataset patDS = cm.getPatientForStudy(studyPk.longValue()); if (log.isDebugEnabled()) { log.debug("Patient Dataset:"); log.debug(patDS); } ds.putAll(patDS.subSet(PAT_ATTR_TAGS)); // Dataset sopInstRef = cm.getSOPInstanceRefMacro(studyPk.longValue(), false); String studyIUID = sopInstRef.getString(Tags.StudyInstanceUID); ds.putUI(Tags.SOPInstanceUID, UIDGenerator.getInstance().createUID()); ds.putUI(Tags.StudyInstanceUID, studyIUID); DcmElement inSq = ds.putSQ(Tags.InputInformationSeq); inSq.addItem(sopInstRef); // Scheduled Human Performer Seq DcmElement schedHPSq = ds.putSQ(Tags.ScheduledHumanPerformersSeq); Dataset item = schedHPSq.addNewItem(); DcmElement hpCodeSq = item.putSQ(Tags.HumanPerformerCodeSeq); Dataset dsCode = (Dataset) this.humanPerformer.get(humanPerformerCode); log.info(dsCode); if (dsCode != null) { hpCodeSq.addItem(dsCode); item.putPN(Tags.HumanPerformerName, dsCode.getString(Tags.CodeMeaning)); } // Scheduled Procedure Step Start Date and Time ds.putDT(Tags.SPSStartDateAndTime, new Date(scheduleDate.longValue())); if (log.isDebugEnabled()) { log.debug("GPSPS Dataset:"); log.debug(ds); } addWorklistItem(ds); } private void addWorklistItem(Dataset ds) { if (ds == null) return; try { getGPWLManager().addWorklistItem(ds); } catch (Exception e) { log.error("Failed to add Worklist Item:", e); } } private GPWLManager getGPWLManager() throws CreateException, RemoteException, HomeFactoryException { return ((GPWLManagerHome) EJBHomeFactory.getFactory().lookup(GPWLManagerHome.class, GPWLManagerHome.JNDI_NAME)) .create(); } private ContentManager getContentManager() throws Exception { ContentManagerHome home = (ContentManagerHome) EJBHomeFactory.getFactory() .lookup(ContentManagerHome.class, ContentManagerHome.JNDI_NAME); return home.create(); } }
/**
* 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());
}
}
/** * @author [email protected] * @version $Revision: 7709 $ $Date: 2008-10-22 11:41:47 -0300 (qua, 22 out 2008) $ */ public class XDSIExportDelegate { private static final String XDSI_DELEGATE_ATTR_NAME = "xdsiDelegate"; private static MBeanServer server; private static ObjectName keyObjectServiceName; private static ObjectName xdsiServiceName; private static final DcmObjectFactory dof = DcmObjectFactory.getInstance(); private static Logger log = Logger.getLogger(XDSIExportDelegate.class.getName()); public XDSIExportDelegate() {} public static final XDSIExportDelegate getInstance(ControllerContext ctx) { HttpSession session = ctx.getRequest().getSession(); XDSIExportDelegate delegate = (XDSIExportDelegate) session.getAttribute(XDSI_DELEGATE_ATTR_NAME); if (delegate == null) { delegate = new XDSIExportDelegate(); try { delegate.init(ctx); } catch (Exception e) { throw new NullPointerException("Cant initialize XDSIExportDelegate!"); } session.setAttribute(XDSI_DELEGATE_ATTR_NAME, delegate); } return delegate; } public void init(ControllerContext ctx) throws Exception { if (keyObjectServiceName != null) return; server = MBeanServerLocator.locate(); String s = ctx.getServletConfig().getInitParameter("keyObjectServiceName"); keyObjectServiceName = new ObjectName(s); s = ctx.getServletConfig().getInitParameter("xdsiServiceName"); xdsiServiceName = new ObjectName(s); } public boolean exportXDSI(XDSIModel xdsiModel) throws Exception { if (xdsiModel.getNumberOfInstances() < 1) { throw new IllegalArgumentException("No Instances selected!"); } Collection items = getObserverContextItems(getAuthorPerson(xdsiModel.getUser())); Dataset rootInfo = getRootInfo(xdsiModel); List contentItems = getContentItems(xdsiModel); contentItems.addAll(items); try { Boolean b; if (!xdsiModel.isPdfExport()) { Dataset keyObjectDS = getKeyObject(xdsiModel.getInstances(), rootInfo, contentItems); b = (Boolean) server.invoke( xdsiServiceName, "sendSOAP", new Object[] {keyObjectDS, xdsiModel.listMetadataProperties()}, new String[] {Dataset.class.getName(), Properties.class.getName()}); } else { String docUID = (String) xdsiModel.getInstances().iterator().next(); b = (Boolean) server.invoke( xdsiServiceName, "exportPDF", new Object[] {docUID, xdsiModel.listMetadataProperties()}, new String[] {String.class.getName(), Properties.class.getName()}); } return b.booleanValue(); } catch (Exception e) { log.warn("Failed to export Selection:", e); throw e; } } public boolean exportPDF(XDSIModel xdsiModel) throws Exception { if (xdsiModel.getNumberOfInstances() < 1) { throw new IllegalArgumentException("No Instances selected!"); } Collection items = getObserverContextItems(getAuthorPerson(xdsiModel.getUser())); Dataset rootInfo = getRootInfo(xdsiModel); List contentItems = getContentItems(xdsiModel); contentItems.addAll(items); String docUID = (String) xdsiModel.getInstances().iterator().next(); try { Boolean b = (Boolean) server.invoke( xdsiServiceName, "exportPDF", new Object[] {docUID, xdsiModel.listMetadataProperties()}, new String[] {String.class.getName(), Properties.class.getName()}); return b.booleanValue(); } catch (Exception e) { log.warn("Failed to export Selection:", e); throw e; } } public boolean createFolder(XDSIModel model) throws Exception { try { Boolean b = (Boolean) server.invoke( xdsiServiceName, "createFolder", new Object[] {model.listMetadataProperties()}, new String[] {Properties.class.getName()}); return b.booleanValue(); } catch (Exception e) { log.warn("Failed to create Folder:", e); throw e; } } 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; } /** * @param user * @return */ public String getAuthorPerson(String user) { try { return (String) server.invoke( xdsiServiceName, "getAuthorPerson", new Object[] {user}, new String[] {String.class.getName()}); } catch (Exception e) { log.warn("Failed to get author person for user " + user + " ! Reason:" + e.getCause()); return null; } } /** * @param xdsiModel * @return */ private List getContentItems(XDSIModel xdsiModel) { List items = new ArrayList(); return items; } /** * @param xdsiModel * @return */ private Dataset getRootInfo(XDSIModel xdsiModel) { Dataset rootInfo = DcmObjectFactory.getInstance().newDataset(); DcmElement sq = rootInfo.putSQ(Tags.ConceptNameCodeSeq); Dataset item = sq.addNewItem(); CodeItem selectedDocTitle = xdsiModel.selectedDocTitle(); item.putSH(Tags.CodeValue, selectedDocTitle.getCodeValue()); item.putSH(Tags.CodingSchemeDesignator, selectedDocTitle.getCodeDesignator()); item.putLO(Tags.CodeMeaning, selectedDocTitle.getCodeMeaning()); return rootInfo; } public Dataset getKeyObject(Collection iuids, Dataset rootInfo, List contentItems) { Object o = null; try { o = server.invoke( keyObjectServiceName, "getKeyObject", new Object[] {iuids, rootInfo, contentItems}, new String[] { Collection.class.getName(), Dataset.class.getName(), Collection.class.getName() }); } catch (RuntimeMBeanException x) { log.warn("RuntimeException thrown in KeyObject Service:" + x.getCause()); throw new IllegalArgumentException(x.getCause().getMessage()); } catch (Exception e) { log.warn("Failed to create Key Object:", e); throw new IllegalArgumentException( "Error: KeyObject Service cant create manifest Key Object! Reason:" + e.getClass().getName()); } return (Dataset) o; } private ContentManager lookupContentManager() throws Exception { ContentManagerHome home = (ContentManagerHome) EJBHomeFactory.getFactory() .lookup(ContentManagerHome.class, ContentManagerHome.JNDI_NAME); return home.create(); } /** @return */ public CodeItem[] getConfiguredAuthorRoles() { return getCodeItems("listAuthorRoles"); } public CodeItem[] getConfiguredClassCodes() { return getCodeItems("listClassCodes"); } public CodeItem[] getConfiguredContentTypeCodes() { return getCodeItems("listContentTypeCodes"); } public CodeItem[] getConfiguredHealthCareFacilityTypeCodes() { return getCodeItems("listHealthCareFacilityTypeCodes"); } public CodeItem[] getConfiguredEventCodes() { return getCodeItems("listEventCodes"); } public CodeItem[] getConfiguredDocTitles() { return getCodeItems("listDocTitleCodes"); } public CodeItem[] getConfiguredConfidentialityCodes() { return getCodeItems("listConfidentialityCodes"); } private CodeItem[] getCodeItems(String methodName) { try { List l = (List) server.invoke(xdsiServiceName, methodName, new Object[] {}, new String[] {}); CodeItem[] items = new CodeItem[l.size()]; for (int i = 0, len = l.size(); i < len; i++) { items[i] = CodeItem.valueofDCM(l.get(i).toString()); // DCM (D)esignator(C)odevalue(M)eaning } return items; } catch (Exception e) { log.error("Failed to get list of configured Codes! method:" + methodName, e); return null; } } /** @return */ public Properties joinMetadataProperties(Properties props) { try { return (Properties) server.invoke( xdsiServiceName, "joinMetadataProperties", new Object[] {props}, new String[] {Properties.class.getName()}); } catch (Exception e) { log.error("Failed to get XDS-I Metadata Properties:", e); return null; } } }
/**
* Implementation of C-DIMSE services.
*
* <p>
*
* <p>Usage:
*
* <p>1. Create a new instance of this class.
*
* <p>2. Use the aASSOCIATE method to establish an association.
*
* <p>3. Use the cFIND method to query the archive.
*
* <p>4. Use the cMOVE method to move an object from the archive to a destination server.
*
* <p>5. Use the cSTORE to store an object into an archive.
*
* <p>6. Use the cECHO to verfy a association.
*
* <p>7. If you are ready with the C-DIMSE services use the aRELEASE method to close the
* association.
*
* <p>
*
* <p>The query/retrieve levels used by C-FIND and C-MOVE are defined as enummerated constants. Use
* the method getQueryRetrieveLevel to convert these values to the String representation used in the
* DICOM element QueryRetrieveLevel (0008,0052).
*
* <p>
*
* <p>Based on dcm4che 1.4.0 sample: MoveStudy.java revision date 2005-10-05
*
* <p>Based on dcm4che 1.4.0 sample: DcmSnd.java revision date 2005-10-05
*
* <p>
*
* <p>See: PS 3.4 - Annex B STORAGE SERVICE CLASS
*
* <p>See: PS 3.4 - Annex C QUERY/RETRIEVE SERVICE CLASS
*
* <p>See: PS 3.4 - C.6 SOP CLASS DEFINITIONS
*
* <p>See: PS 3.4 - C.6.2 Study Root SOP Class Group
*
* <p>
*
* <p>Details of how to run the services is given in a configuration property file. A sample may be
* found at "./resources/CDimseService.cfg".
*
* @author Thomas Hacklaender
* @version 2006-08-28
*/
public class CDimseService {
static final Logger log = Logger.getLogger("CDimseService");
/** The DEBUG flag is set, if the logging level of this class is Debug */
static final boolean DEBUG = log.isDebugEnabled();
// >>>> Factorys >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
private static final UIDDictionary uidDict =
DictionaryFactory.getInstance().getDefaultUIDDictionary();
private static final AssociationFactory aFact = AssociationFactory.getInstance();
private static final DcmObjectFactory oFact = DcmObjectFactory.getInstance();
private static final DcmParserFactory pFact = DcmParserFactory.getInstance();
private static final DcmObjectFactory dof = DcmObjectFactory.getInstance();
/** Default AE title used for the association if it is not explicit given in the url filed. */
private static final String DEFAULT_CALLING_AET = "OVIYAM";
/** Query/Retrieve Level Values for Study = "PATIENT". See PS 3.4 - C.6 SOP CLASS DEFINITIONS */
public static final int PATIENT_LEVEL = 0;
/** Query/Retrieve Level Values for Study = "STUDY". See PS 3.4 - C.6. SOP CLASS DEFINITIONS */
public static final int STUDY_LEVEL = 1;
/** Query/Retrieve Level Values for Series = "SERIES". See PS 3.4 - C.6 SOP CLASS DEFINITIONS */
public static final int SERIES_LEVEL = 2;
/** Query/Retrieve Level Values for Image = "IMAGE". See PS 3.4 - C.6 SOP CLASS DEFINITIONS */
public static final int IMAGE_LEVEL = 3;
PresContext pc;
/**
* DICOM URL to define a communication partner for an association.
*
* <p>PROTOCOL://CALLED[:CALLING]@HOST[:PORT]
*
* <p>
*
* <p>PROTOCOL Specifies protocol. Possible values:
*
* <p>- dicom DICOM default (without TLS)
*
* <p>- dicom-tls DICOM on TLS (offer AES and DES encryption)
*
* <p>- dicom-tls.aes DICOM on TLS (force AES or DES encryption)
*
* <p>- dicom-tls.3des DICOM on TLS (force DES encryption)
*
* <p>- dicom-tls.nodes DICOM on TLS (no encryption)
*
* <p>CALLED Called AET in association request (max 16 chars)
*
* <p>CALLING Calling AET in association request (max 16 chars) [default id final field
* DEFAULT_CALLING_AET = MYAET]
*
* <p>HOST Name or IP address of host, where the server is running
*
* <p>PORT TCP port address, on which the server is listing for
*
* <p>incoming TCP Transport Connection Indication [default=104]
*/
private DcmURL url = null;
/** Message priority. Possible values Command.LOW = 2, Command.MEDIUM = 0, Command.HIGH = 1 */
private int priority = Command.MEDIUM;
/**
* Time-out waiting [in msec] for A-ASSOCIATE-AC acknowlage, 0 is interpreted as an infinite
* timeout [default=5000].
*/
private int acTimeout = 5000;
/**
* Time-out waiting [in msec] for DIMSE on aASSOCIATE association, 0 is interpreted as an infinite
* timeout [default=0].
*/
private int dimseTimeout = 0;
/** Time delay [in msec] for socket aRELEASE after sending A-ABORT [default=500]. */
private int soCloseDelay = 500;
/**
* Association Request package (A-ASSOCIATE-RQ) is part of the connection service ACSE
* (Association Control Service Element). In TCP/IP networks connection services are emulated by
* the "DICOM Upper Layer Service". This presentation srvice encapsulats the data in PDUs
* (Protocol Data Unit).
*/
private AAssociateRQ assocRQ = aFact.newAAssociateRQ();
/** Association object for establishing an active association. */
private Association assoc = null;
/** Accepted association */
private ActiveAssociation aassoc = null;
/**
* Activates packing of command PDV (Presentation Data Value) + (first) data PDV into one
* P-DATA-TF PDU (Protocol Data Unit)
*/
private boolean packPDVs = false;
/** TLS context. Set by method initTLS */
private SSLContextAdapter tls = null;
/** An array of implemented ciphers for the communication protocol (given in url). */
private String[] cipherSuites = null;
/**
* Specifies Key Attributes used for C-FIND. Wildcards '*','?', '-' and '\' are allowed as
* element-values (see PS 3.4 - C.2.2.2 Attribute Matching). If an key attribute is defined, but
* has an empty value, it matches every value at the storage side.
*
* <p>Key attributes have a type (PS 3.4 - C.2.2.1 Attribute Types)
*
* <p>- U = one Attribute shall be defined as a Unique Key.
*
* <p>- R = a set of Attributes shall be defined as Required Keys.
*
* <p>- O = a set of Attributes shall be defined as Optional Keys.
*
* <p>The complete list of Key Attributes can be found at PS 3.4 - C.6.2 Study Root SOP Class
* Group.
*
* <p>As a result of C-FIND for each matching item in the archive a DIMSE object containing the
* Key Attributes is send back. In this object the Key Attributes are set corresponding to values
* found in the archive. Attributes of type "O" may be send back with empty value. Only used by
* C-FIND.
*/
private Dataset keys = dof.newDataset();
/**
* Application Entity Title (AET) of the destination for the C-MOVE. The AET must be known by the
* archive together with the host IP adress and the port number. Only used by C-MOVE.
*/
private String dest;
// >>>> Constructor >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
/**
* Constructor for the StorageSCUServiceClass object. Initializes everything.
*
* <p>Details of how to run the server is given in another configuration property file. A sample
* may be found at "./resources/StorageSCUServiceClass.cfg".
*
* @param cfg the configuration properties for this class.
* @param url the DcmURL of the communication partner.
* @throws ParseException
*/
public CDimseService(ConfigProperties cfg, DcmURL url) throws ParseException {
this.url = url;
this.priority = Integer.parseInt(cfg.getProperty("prior", "0"));
this.packPDVs = "true".equalsIgnoreCase(cfg.getProperty("pack-pdvs", "false"));
initAssocParam(cfg, url);
// initEchoAssocParam(cfg, url);
initTLS(cfg);
// Only used by C-FIND
initKeys(cfg);
// Only used by C-MOVE
this.dest = cfg.getProperty("dest");
}
// >>>> Methods >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
/**
* Initializes Association related parameters.
*
* @param cfg the configuration properties for this class.
* @param url the DcmURL of the communication partner.
*/
private final void initAssocParam(ConfigProperties cfg, DcmURL url) {
String callingAET = null;
// >>>> Get data for filling the Association object for establishing an
// >>>> active association from configuration file
acTimeout = Integer.parseInt(cfg.getProperty("ac-timeout", "5000"));
dimseTimeout = Integer.parseInt(cfg.getProperty("dimse-timeout", "0"));
soCloseDelay = Integer.parseInt(cfg.getProperty("so-close-delay", "500"));
// >>>> Fill the Association Request package (A-ASSOCIATE-RQ)
// Identifying the communication partner by an AET (Application Entity Title)
assocRQ.setCalledAET(url.getCalledAET());
// Identifying ourselves by an AET (Application Entity Title)
if (url.getCallingAET() != null) {
callingAET = url.getCallingAET();
} else {
callingAET = DEFAULT_CALLING_AET;
}
assocRQ.setCallingAET(callingAET);
// Maximum size of one PDU (Protocol Data Unit)
assocRQ.setMaxPDULength(Integer.parseInt(cfg.getProperty("max-pdu-len", "16352")));
// Defines possibilities for asynchron DIMSE communication. Noramly synchron DIMSE communication
// is used.
// API doc: AssociationFactory.newAsyncOpsWindow(int maxOpsInvoked, int maxOpsPerfomed)
// PS 3.7 - Annex D.3.3.3 ASYNCHRONOUS OPERATIONS WINDOW NEGOTIATION
// maxOpsInvoked: This field shall contain the Maximum-number-operationsinvoked as defined for
// the Association-requester
// maxOpsPerfomed: This field shall contain the Maximum-number-operationsperformed as defined
// for the Association-requester
assocRQ.setAsyncOpsWindow(
aFact.newAsyncOpsWindow(Integer.parseInt(cfg.getProperty("max-op-invoked", "0")), 1));
for (Enumeration it = cfg.keys(); it.hasMoreElements(); ) {
String key = (String) it.nextElement();
// Setup available transfer syntaces for storage SOP classes
// PS 3.4 - Annex B STORAGE SERVICE CLASS
// PS 3.4 - B.5 STANDARD SOP CLASSES
if (key.startsWith("pc.")) {
initPresContext(
Integer.parseInt(key.substring(3)),
cfg.tokenize(cfg.getProperty(key), new LinkedList()));
}
}
}
/**
* Only used by method initAssocParam: Sets up available transfer syntaces for storage SOP
* classes.
*
* @param pcid is a for the association unique odd number between 1 and 255.
* @param val a list: First element is the symbolic name of the UID of the SOP to transmit, the
* following elements are the supportet transfer syntax for that SOP.
*/
private final void initPresContext(int pcid, List val) {
Iterator it = val.iterator();
String as = UIDs.forName((String) it.next());
String[] tsUIDs = new String[val.size() - 1];
for (int i = 0; i < tsUIDs.length; ++i) {
tsUIDs[i] = UIDs.forName((String) it.next());
}
// API doc: AssociationFactory.newPresContext(int pcid, String asuid, String[] tsuid)
// pcid is a for the association unique odd number between 1 and 255.
// asuid is the UID of a SOP class
// TS list of transfer syntaces supported by this class for asuid.
assocRQ.addPresContext(aFact.newPresContext(pcid, as, tsUIDs));
}
/**
* Initializes TLS (Transport Layer Security, predecessor of SSL, Secure Sockets Layer) connection
* related parameters. TLS expects RSA (Ron Rivest, Adi Shamir and Len Adleman) encoded keys and
* certificates.
*
* <p>Keys and certificates may be stored in PKCS #12 (Public Key Cryptography Standards) or JKS
* (Java Keystore) containers.
*
* <p>TSL is used to encrypt data during transmission, which is accomplished when the connection
* between the two partners A (normally the client) and B (normally the server) is established. If
* A asks B to send TSL encrypted data, both partners exchange some handshake information. In a
* first step B tries to authentify itself against A (server authentification, optional in TSL but
* implementet in this way in dcm4che). For that B presents its public key for A to accept or
* deny. If the authentification is accepted, A tries to authentify itself against B (client
* authentification, optional in TSL but implementet in this way in dcm4che).If B accepts the
* authentification A and B agree on a hash (symmetric key, which is independent of the
* private/public keys used for authentification) for the duration of their conversation, which is
* used to encrypt the data.
*
* <p>To be able to establish a TSL connection B needs a privat/public key pair, which identifies
* B unambiguously. For that the private key is generated first; than the root-public key is
* derived from that private key. To bind the root-public key with the identity of B a Certificate
* Authority (CA) is used: The root-public key is send to CA, which returns a certified-public
* key, which includes information about the CA as well as the root-public key. Optionally this
* process can be repeated several times so that the certified-public key contains a chain of
* certificates of different CA's.
*
* <p>The certified-public key of B is presented to A during server authentification. Partner A
* should accept this key, if it can match the last certificate in the chain with a
* root-certificat found in its local list of root-certificates of CA's. That means, that A does
* not check the identity of B, but "trusts" B because it was certified by an authority. The same
* happens for client authentification. Handling of authentification of the identity of the
* communication partner is subject of PS 3.15 - Security and System Management Profiles.
*
* <p>In the configuration files of this method the certified-public key is stored in the property
* "tls-key" and the root-certificates of the known CA's in "tls-cacerts".
*
* <p>Usually the certified-public keys of A and B are different, but they also may be the same.
* In this case the root-certificates are also the same.
*
* <p>It is possible to establish a TLS connection without using a CA: In this case both partners
* creates a individual container holding their private and root-public key. These containers
* could be used for certifying also, because the length of the certifying chain is one and
* therefore the root-public key is also the last certified-public key. Therefore the root-public
* key works in this scenario also as the root-certificate of the "certifying authoroty".
*
* <p>If no keystores are specified in the configuration properties, the not-certified
* default-keystore "resources/identityJava.jks" is used for "tls-key" and "tls-cacerts" when
* establishing the connection.
*
* @param cfg the configuration properties for this class.
* @throws ParseException
*/
private void initTLS(ConfigProperties cfg) throws ParseException {
char[] keystorepasswd;
char[] keypasswd;
char[] cacertspasswd;
URL keyURL;
URL cacertURL;
String value;
try {
// Cipher suites for protokoll:
// dicom = null
// dicom-tls = SSL_RSA_WITH_NULL_SHA, TLS_RSA_WITH_AES_128_CBC_SHA,
// SSL_RSA_WITH_3DES_EDE_CBC_SHA
// dicom-tls.3des = SSL_RSA_WITH_3DES_EDE_CBC_SHA
// dicom-tls.aes = TLS_RSA_WITH_AES_128_CBC_SHA, SSL_RSA_WITH_3DES_EDE_CBC_SHA
// dicom-tls.nodes = SSL_RSA_WITH_NULL_SHA
cipherSuites = url.getCipherSuites();
if (cipherSuites == null) {
return;
}
// Get a new TLS context
tls = SSLContextAdapter.getInstance();
// >>>> Managing the keystore file containing the privat key and
// >>>> certified-public key to establish the communication
// Password of the keystore [default: secret]
keystorepasswd = cfg.getProperty("tls-keystore-passwd", "secret").toCharArray();
// Password of the private key [default: secret]
keypasswd = cfg.getProperty("tls-key-passwd", "secret").toCharArray();
// URL of the file containing the default-keystore
keyURL = CDimseService.class.getResource("/resources/identityJava.jks");
// If availabel, replace URL with the one specified in the configuration file
if ((value = cfg.getProperty("tls-key")) != null) {
try {
// Property specified, try to set to specified value
keyURL = ConfigProperties.fileRefToURL(CDimseService.class.getResource(""), value);
} catch (Exception e) {
log.warn("Wrong value for tls-key: " + value + ". tls-key was set to default value.");
}
}
// log.info("Key URL: " + keyURL.toString());
// Sets the key attribute of the SSLContextAdapter object
// API doc: SSLContextAdapter.loadKeyStore(java.net.URL url, char[] password)
// API doc: SSLContextAdapter.setKey(java.security.KeyStore key, char[] password)
tls.setKey(tls.loadKeyStore(keyURL, keystorepasswd), keypasswd);
// >>>> Managing the keystore containing the root-certificates of the Ceritifying Authorities
// >>>> used for signing the public key
// Password of the keystore [default: secret]
cacertspasswd = cfg.getProperty("tls-cacerts-passwd", "secret").toCharArray();
// URL of the file containing the default-keystore
cacertURL = CDimseService.class.getResource("/resources/identityJava.jks");
// If availabel, replace URL with the one specified in the configuration file
if ((value = cfg.getProperty("tls-cacerts")) != null) {
try {
// Property specified, try to set to specified value
cacertURL = ConfigProperties.fileRefToURL(CDimseService.class.getResource(""), value);
} catch (Exception e) {
log.warn(
"Wrong value for tls-cacerts: " + value + ". tls-cacerts was set to default value.");
}
}
// log.info("Root-certificat of CA URL: " + cacertURL.toString());
// Sets the trust attribute of the SSLContextAdapter object
// API doc: SSLContextAdapter.loadKeyStore(java.net.URL url, char[] password)
// API doc: SSLContextAdapter.setTrust(java.security.KeyStore cacerts)
tls.setTrust(tls.loadKeyStore(cacertURL, cacertspasswd));
// Init TLS context adapter
tls.init();
} catch (Exception ex) {
throw new ParseException("Could not initalize TLS configuration.", 0);
}
}
/**
* 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);
}
/**
* Add the query keys found in the configuration properties to the Dataset "keys" used bei the
* cFIND method.
*
* @param cfg the configuration properties for this class.
* @throws ParseException if a given properties for the keys was not found.
*/
private void addQueryKeys(ConfigProperties cfg) throws ParseException {
// Add/replace keys found in the configuration file. Syntax key.<element name> = <element value>
for (Enumeration it = cfg.keys(); it.hasMoreElements(); ) {
String key = (String) it.nextElement();
if (key.startsWith("key.")) {
try {
keys.putXX(Tags.forName(key.substring(4)), cfg.getProperty(key));
} catch (Exception e) {
throw new ParseException(
"Illegal entry in configuration filr: " + key + "=" + cfg.getProperty(key), 0);
}
}
}
}
/**
* Sets the Dataset representing the query keys in C-FIND. The user can specify concret values to
* limit the search.
*
* <p>Wildcards '*','?', '-' and '\' are allowed as element-values (see PS 3.4 - C.2.2.2 Attribute
* Matching). If an key attribute is defined, but has an empty value, it matches every value at
* the storage side.
*
* <p>At a minimum the key "QueryRetrieveLevel" must be set ("STUDY", "SERIES" or "IMAGE"). See PS
* 3.4 - C.6.2 Study Root SOP Class Group
*
* <p>As the result for C-FIND these keys are filled with the values found in the archive.
*
* @param ds the Dataset containig the search keys.
*/
public void setQueryKeys(Dataset ds) {
keys = ds;
}
/**
* Sets the Dataset representing the query keys in C-FIND. The user can specify concret values to
* limit the search.
*
* <p>Wildcards '*','?', '-' and '\' are allowed as element-values (see PS 3.4 - C.2.2.2 Attribute
* Matching). If an key attribute is defined, but has an empty value, it matches every value at
* the storage side.
*
* <p>At a minimum the key "QueryRetrieveLevel" must be set ("STUDY", "SERIES" or "IMAGE"). See PS
* 3.4 - C.6.2 Study Root SOP Class Group
*
* <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.
*/
public void setQueryKeys(ConfigProperties cfg) throws ParseException {
// Remove all keys
keys = dof.newDataset();
// Add the keys found in the configuration properties
addQueryKeys(cfg);
}
/**
* Starts a active association to a communication partner. See PS 3.8 - 7.1 A-ASSOCIATE SERVICE
*
* @return true, if association was successful established.
* @exception ConnectException
* @exception IOException
* @exception GeneralSecurityException
*/
public boolean aASSOCIATE() throws ConnectException, IOException, GeneralSecurityException {
// No association may be active
if (assoc != null) {
throw new ConnectException("Association already established");
}
// New Association object for establishing an active association
assoc = aFact.newRequestor(newSocket(url.getHost(), url.getPort()));
// >>>> Fill the Association object with relevant data
assoc.setAcTimeout(acTimeout);
assoc.setDimseTimeout(dimseTimeout);
assoc.setSoCloseDelay(soCloseDelay);
assoc.setPackPDVs(packPDVs);
// 1. Create an communication channel to the communication partner defined in the Association
// object
// 2. Send the A-ASSOCIATE-RQ package
// 3. Receive the aAssociation acknowlage/reject package from the communication partner as a PDU
// (Protocol Data Unit)
PDU assocAC = assoc.connect(assocRQ);
if (!(assocAC instanceof AAssociateAC)) {
// Acknowlage is A-ASSOCIATE-RJ
// Association rejected
assoc = null;
// Return aASSOCIATE faild
return false;
}
// Acknowlage is A-ASSOCIATE_AC
// Association accepted
// Start the accepted association
// API doc: AssociationFactory.newActiveAssociation(Association assoc, DcmServiceRegistry
// services)
aassoc = aFact.newActiveAssociation(assoc, null);
aassoc.start();
// Return successfull opened
return true;
}
/**
* Creates a stream socket and connects it to the specified port number on the named host.
*
* @param host the IP address.
* @param port the port number.
* @return the Socket.
* @exception IOException
* @exception GeneralSecurityException
*/
private Socket newSocket(String host, int port) throws IOException, GeneralSecurityException {
// Test, if a secured connection is needed
if (cipherSuites != null) {
// Creates a socket for secured connection.
// The SSLContextAdapter tls uses the javax.net.ssl package for establishing
// the connection.
return tls.getSocketFactory(cipherSuites).createSocket(host, port);
} else {
// Creates a standard Java socket for unsecured connection.
return new Socket(host, port);
}
}
/**
* Releases the active association. See PS 3.8 - 7.2 A-RELEASE SERVICE
*
* @param waitOnRSP if true, method waits until it receives the responds to the release request.
* @exception InterruptedException Description of the Exception
* @exception IOException Description of the Exception
*/
public void aRELEASE(boolean waitOnRSP) throws InterruptedException, IOException {
if (assoc != null) {
try {
aassoc.release(waitOnRSP);
} finally {
assoc = null;
aassoc = null;
}
}
}
/**
* Stores a DICOM object in an archive (Storage SCP).
*
* <p>See PS 3.4 - Annex B STORAGE SERVICE CLASS.
*
* @param ds the Dataset to store.
* @throws ConnectException
* @throws ParseException
* @throws IOException
* @throws InterruptedException
* @throws IllegalStateException
*/
public void cSTORE(Dataset ds)
throws InterruptedException, IOException, ConnectException, ParseException {
String sopClassUID;
String sopInstUID;
PresContext pc = null;
// An association must be active
if (aassoc == null) {
throw new ConnectException("No Association established");
}
// SOP Class UID must be given
if ((sopClassUID = ds.getString(Tags.SOPClassUID)) == null) {
throw new ParseException("No SOP Class UID in Dataset", 0);
}
// SOP Instance UID must be given
if ((sopInstUID = ds.getString(Tags.SOPInstanceUID)) == null) {
throw new ParseException("No SOP Instance UID in Dataset", 0);
}
// Test, if applicable presentation context was found
if ((pc =
aassoc
.getAssociation()
.getAcceptedPresContext(sopClassUID, UIDs.ImplicitVRLittleEndian))
== null
&& (pc =
aassoc
.getAssociation()
.getAcceptedPresContext(sopClassUID, UIDs.ExplicitVRLittleEndian))
== null
&& (pc =
aassoc
.getAssociation()
.getAcceptedPresContext(sopClassUID, UIDs.ExplicitVRBigEndian))
== null) {
throw new ConnectException("No applicable presentation context found");
}
// New Cammand Set, see: DICOM Part 7: Message Exchange, 6.3.1 Command Set Structure
Command cStoreRQ = oFact.newCommand();
// API doc: Command.initCStoreRQ(int msgID, String sopClassUID, String sopInstUID, int priority)
cStoreRQ.initCStoreRQ(assoc.nextMsgID(), sopClassUID, sopInstUID, priority);
// API doc: AssociationFactorynewDimse(int pcid, Command cmd, Dataset ds)
// DIMSE (DICOM Message Service Element) ist ein Nachrichtendienst in DICOM
Dimse storeRq = aFact.newDimse(pc.pcid(), cStoreRQ, ds);
// PS 3.7 - 9.3.1 C-STORE PROTOCOL, 9.3.1.2 C-STORE-RSP
// Always returns SUCESS result code.
// Invoke active association with echo request Dimse
FutureRSP future = aassoc.invoke(storeRq);
System.out.println("store is going in this AE");
// Response to the C-ECHO request.
// The result cannot be accessed until it has been set.
Dimse storeRsp = future.get();
Command rspCmd = storeRsp.getCommand();
// PS 3.7 - 9.3.5 C-MOVE PROTOCOL, 9.3.5.2 C-ECHO-RSP
int status = rspCmd.getStatus();
switch (status) {
case 0x0000:
// Success
break;
default:
log.error("C-STORE failed: " + Integer.toHexString(status));
break;
}
}
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;
}
/**
* Queries the archive for DICOM objects matching Attribute Keys defined in the loacal field
* "keys". This field is set by the constructor out of the configuration parameters or by the
* methods setQueryKeys(Configuration) and setQueryKeys(Dataset). See PS 3.4 - Annex C
* QUERY/RETRIEVE SERVICE CLASS.
*
* <p>The method returns, when the result is received from the communication partner.
*
* @return the result of the cFIND as a Vector of Dataset objects each specifying one matching
* DICOM object. If no matching objects are found an empty Vector is returned.
* @throws ConnectException
* @throws IOException
*/
public Vector cFIND() throws ConnectException, IOException, InterruptedException {
List dimseList;
Vector datasetVector;
// An association must be active
if (aassoc == null) {
throw new ConnectException("No Association established");
}
// Test, if Presentation Context for C-FIND is supported
// API doc: Association.getAcceptedPresContext(String asuid, String tsuid)
// UIDs.StudyRootQueryRetrieveInformationModelGET
if ((pc =
aassoc
.getAssociation()
.getAcceptedPresContext(
UIDs.StudyRootQueryRetrieveInformationModelFIND,
UIDs.ExplicitVRLittleEndian))
== null
&& (pc =
aassoc
.getAssociation()
.getAcceptedPresContext(
UIDs.StudyRootQueryRetrieveInformationModelFIND,
UIDs.ImplicitVRLittleEndian))
== null) {
throw new ConnectException(
"Association does not support presentation context for StudyRootQueryRetrieveInformationModelFIND SOP.");
}
// New Cammand Set, see: DICOM Part 7: Message Exchange, 6.3.1 Command Set Structure
Command rqCmd = dof.newCommand();
// API doc: Command.initCFindRQ(int msgID, String sopClassUID, int priority)
rqCmd.initCFindRQ(assoc.nextMsgID(), UIDs.StudyRootQueryRetrieveInformationModelFIND, priority);
// API doc: AssociationFactorynewDimse(int pcid, Command cmd, Dataset ds)
// DIMSE (DICOM Message Service Element) ist ein Nachrichtendienst in DICOM
Dimse findRq = aFact.newDimse(pc.pcid(), rqCmd, keys);
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
FutureRSP future = aassoc.invoke(findRq);
// Response to the C-FIND request.
// The result cannot be accessed until it has been set.
Dimse findRsp = future.get();
// 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());
}
return datasetVector;
}
/**
* Ask archive to move one DICOM object to the destination (C-MOVE). See PS 3.4 - Annex C
* QUERY/RETRIEVE SERVICE CLASS.
*
* <p>Use the Study Root Query/Retrieve Information Model to communicate with the archive. See PS
* 3.4 - C.6.2 Study Root SOP Class Group.
*
* <p>PS 3.4 - C.4.2.1.4.1 Request Identifier Structure (for C-MOVE): An Identifier in a C-MOVE
* request shall contain:
*
* <p>- the Query/Retrieve Level (0008,0052) which defines the level of the retrieval
*
* <p>- Unique Key Attributes which may include Patient ID, Study Instance UIDs, Series Instance
* UIDs, and the SOP Instance UIDs
*
* <p>PS 3.4 - C.4.2.2.1 Baseline Behavior of SCU (of C-MOVE):
*
* <p>The SCU shall supply a single value in the Unique Key Attribute for each level above the
* Query/Retrieve level. For the level of retrieve, the SCU shall supply one unique key if the
* level of retrieve is above the STUDY level and shall supply one UID, or a list of UIDs if a
* retrieval of several items is desired and the retrieve level is STUDY, SERIES or IMAGE.
*
* @param ds the DICOM object represented as a Dataset.
* @return a result-code: 0x0000 = SUCCESS sub-operations complete no failures, 0xB000 = WARNING
* sub-operations complete one or more failures, other = errors defined in PS 3.4 - C.4.2.1.5
* Status
* @throws ConnectException
* @throws InterruptedException
* @throws IOException
*/
public Vector cMOVE(Dataset ds) throws ConnectException, InterruptedException, IOException {
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.StudyRootQueryRetrieveInformationModelMOVE,
UIDs.ExplicitVRLittleEndian))
== null
&& (pc =
aassoc
.getAssociation()
.getAcceptedPresContext(
UIDs.StudyRootQueryRetrieveInformationModelMOVE,
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.StudyInstanceUID);
// 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.initCMoveRQ(
assoc.nextMsgID(), UIDs.StudyRootQueryRetrieveInformationModelMOVE, priority, dest);
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.StudyInstanceUID, 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();
Dataset dds = moveRsp.getDataset();
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
Dimse dms = future.get();
// >>>> 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;
}
/**
* Implements the ECHO service. The C-ECHO service is invoked by a DIMSE-service-user to verify
* end-to-end communications with a peer DIMSE-service-user. See PS 3.7 - 9.1.5 C-ECHO SERVICE
*
* @exception ConnectException
* @exception InterruptedException
* @exception IOException
*/
public long cECHO() throws ConnectException, InterruptedException, IOException {
PresContext pc;
long t1 = System.currentTimeMillis();
// An association must be active
if (aassoc == null) {
throw new ConnectException("No Association established");
}
// Test, if Presentation Context for C-ECHO is supported
// API doc: Association.getAcceptedPresContext(String asuid, String tsuid)
if ((pc =
aassoc
.getAssociation()
.getAcceptedPresContext(UIDs.Verification, UIDs.ImplicitVRLittleEndian))
== null) {
throw new ConnectException(
"Association does not support presentation context: Verification SOP/ImplicitVRLittleEndian.");
}
// New Cammand Set, see: DICOM Part 7: Message Exchange, 6.3.1 Command Set Structure
Command cEchoRQ = oFact.newCommand();
// API doc: Command.initCEchoRQ(int msgID)
cEchoRQ.initCEchoRQ(1);
// API doc: AssociationFactorynewDimse(int pcid, Command cmd)
// DIMSE (DICOM Message Service Element) ist ein Nachrichtendienst in DICOM
Dimse echoRq = aFact.newDimse(pc.pcid(), cEchoRQ);
// PS 3.7 - 9.3.5 C-ECHO PROTOCOL, 9.3.5.2 C-ECHO-RSP
// Always returns SUCESS result code.
// Invoke active association with echo request Dimse
FutureRSP future = aassoc.invoke(echoRq);
// Response to the C-ECHO request.
// The result cannot be accessed until it has been set.
Dimse echoRsp = future.get();
Command rspCmd = echoRsp.getCommand();
// PS 3.7 - 9.3.5 C-MOVE PROTOCOL, 9.3.5.2 C-ECHO-RSP
int status = rspCmd.getStatus();
switch (status) {
case 0x0000:
// Success
break;
default:
log.error("C-ECHO failed: " + Integer.toHexString(status));
break;
}
return System.currentTimeMillis() - t1;
}
/**
* Gets the String value used for DICOM element QueryRetrieveLevel (0008,0052).
*
* <p>See PS 3.4 - C.6 SOP CLASS DEFINITIONS
*
* @param queryRetrieveLevel query/retrieve level as a enumerated value.
* @return the String value assiciated to enumerated query/retrieve level.
*/
public static String getQueryRetrieveLevel(int queryRetrieveLevel) {
switch (queryRetrieveLevel) {
case PATIENT_LEVEL:
return "PATIENT";
case STUDY_LEVEL:
return "STUDY";
case SERIES_LEVEL:
return "SERIES";
case IMAGE_LEVEL:
return "IMAGE";
default:
return "";
}
}
}
/**
* Stores a DICOM object in an archive (Storage SCP).
*
* <p>See PS 3.4 - Annex B STORAGE SERVICE CLASS.
*
* @param ds the Dataset to store.
* @throws ConnectException
* @throws ParseException
* @throws IOException
* @throws InterruptedException
* @throws IllegalStateException
*/
public void cSTORE(Dataset ds)
throws InterruptedException, IOException, ConnectException, ParseException {
String sopClassUID;
String sopInstUID;
PresContext pc = null;
// An association must be active
if (aassoc == null) {
throw new ConnectException("No Association established");
}
// SOP Class UID must be given
if ((sopClassUID = ds.getString(Tags.SOPClassUID)) == null) {
throw new ParseException("No SOP Class UID in Dataset", 0);
}
// SOP Instance UID must be given
if ((sopInstUID = ds.getString(Tags.SOPInstanceUID)) == null) {
throw new ParseException("No SOP Instance UID in Dataset", 0);
}
// Test, if applicable presentation context was found
if ((pc =
aassoc
.getAssociation()
.getAcceptedPresContext(sopClassUID, UIDs.ImplicitVRLittleEndian))
== null
&& (pc =
aassoc
.getAssociation()
.getAcceptedPresContext(sopClassUID, UIDs.ExplicitVRLittleEndian))
== null
&& (pc =
aassoc
.getAssociation()
.getAcceptedPresContext(sopClassUID, UIDs.ExplicitVRBigEndian))
== null) {
throw new ConnectException("No applicable presentation context found");
}
// New Cammand Set, see: DICOM Part 7: Message Exchange, 6.3.1 Command Set Structure
Command cStoreRQ = oFact.newCommand();
// API doc: Command.initCStoreRQ(int msgID, String sopClassUID, String sopInstUID, int priority)
cStoreRQ.initCStoreRQ(assoc.nextMsgID(), sopClassUID, sopInstUID, priority);
// API doc: AssociationFactorynewDimse(int pcid, Command cmd, Dataset ds)
// DIMSE (DICOM Message Service Element) ist ein Nachrichtendienst in DICOM
Dimse storeRq = aFact.newDimse(pc.pcid(), cStoreRQ, ds);
// PS 3.7 - 9.3.1 C-STORE PROTOCOL, 9.3.1.2 C-STORE-RSP
// Always returns SUCESS result code.
// Invoke active association with echo request Dimse
FutureRSP future = aassoc.invoke(storeRq);
System.out.println("store is going in this AE");
// Response to the C-ECHO request.
// The result cannot be accessed until it has been set.
Dimse storeRsp = future.get();
Command rspCmd = storeRsp.getCommand();
// PS 3.7 - 9.3.5 C-MOVE PROTOCOL, 9.3.5.2 C-ECHO-RSP
int status = rspCmd.getStatus();
switch (status) {
case 0x0000:
// Success
break;
default:
log.error("C-STORE failed: " + Integer.toHexString(status));
break;
}
}
/**
* @author franz.willer
* <p>TODO To change the template for this generated type comment go to Window - Preferences -
* Java - Code Style - Code Templates
*/
public class ECGSupport {
public static final String CONTENT_TYPE_SVGXML = "image/svg+xml";
private static Logger log = Logger.getLogger(ECGSupport.class.getName());
private static final DcmObjectFactory factory = DcmObjectFactory.getInstance();
private RIDSupport ridSupport;
private RIDStorageDelegate storage = RIDStorageDelegate.getInstance();
public ECGSupport(RIDSupport ridSupport) {
this.ridSupport = ridSupport;
}
/**
* @param reqObj
* @param ds
* @return
*/
public RIDResponseObject getECGDocument(RIDRequestObject reqObj, Dataset ds) {
String contentType = reqObj.getParam("preferredContentType");
if (contentType.equals(CONTENT_TYPE_SVGXML) || contentType.equals("image/svg")) {
contentType = CONTENT_TYPE_SVGXML;
if (ridSupport.checkContentType(reqObj, new String[] {CONTENT_TYPE_SVGXML}) == null) {
return new RIDStreamResponseObjectImpl(
null,
RIDSupport.CONTENT_TYPE_HTML,
HttpServletResponse.SC_BAD_REQUEST,
"Display actor doesnt accept preferred content type!");
}
} else if (contentType.equals(RIDSupport.CONTENT_TYPE_PDF)) {
if (ridSupport.checkContentType(reqObj, new String[] {RIDSupport.CONTENT_TYPE_PDF}) == null) {
return new RIDStreamResponseObjectImpl(
null,
RIDSupport.CONTENT_TYPE_HTML,
HttpServletResponse.SC_BAD_REQUEST,
"Display actor doesnt accept preferred content type!");
}
} else {
return new RIDStreamResponseObjectImpl(
null,
RIDSupport.CONTENT_TYPE_HTML,
HttpServletResponse.SC_NOT_ACCEPTABLE,
"preferredContentType '"
+ contentType
+ "' is not supported! Only 'application/pdf' and 'image/svg+xml' are supported !");
}
String docUID = reqObj.getParam("documentUID");
log.info("get ECG document! docUID:" + docUID);
BaseDocument doc = storage.getDocument(docUID, contentType);
try {
if (doc != null) {
return new RIDStreamResponseObjectImpl(
doc.getInputStream(), contentType, HttpServletResponse.SC_OK, null);
}
} catch (Exception x) {
log.error("Getting InputStream for RID Response of document " + docUID + " failed!", x);
}
try {
Dataset fullDS = getDataset(ds);
doc = storage.createDocument(docUID, contentType);
if (fullDS == null) {
return new RIDStreamResponseObjectImpl(
null,
RIDSupport.CONTENT_TYPE_HTML,
HttpServletResponse.SC_NOT_FOUND,
"Requested document not found::" + ds.getString(Tags.SOPClassUID));
} else {
if (contentType.equals(RIDSupport.CONTENT_TYPE_PDF)) {
return handlePDF(fullDS, doc);
} else {
return handleSVG(fullDS, doc);
}
}
} catch (Exception e) {
return new RIDStreamResponseObjectImpl(
null,
RIDSupport.CONTENT_TYPE_HTML,
HttpServletResponse.SC_INTERNAL_SERVER_ERROR,
"Internal server error:" + e.getMessage());
}
}
/**
* @param string
* @return
* @throws NeedRedirectionException
* @throws IOException
*/
private Dataset getDataset(Dataset ds) throws IOException {
String iuid = ds.getString(Tags.SOPInstanceUID);
File file = ridSupport.getDICOMFile(iuid);
if (log.isDebugEnabled())
log.debug("DCM file for " + ds.getString(Tags.SOPInstanceUID) + ":" + file);
if (file == null) return null;
Dataset dsFile;
if (!ridSupport.isUseOrigFile()) {
FileDataSource dsrc = null;
try {
dsrc =
(FileDataSource)
ridSupport
.getMBeanServer()
.invoke(
ridSupport.getQueryRetrieveScpName(),
"getDatasourceOfInstance",
new Object[] {iuid},
new String[] {String.class.getName()});
} catch (Exception e) {
log.error("Failed to get updated DICOM file", e);
}
file = new File(file + ".dcm");
file.deleteOnExit();
OutputStream os = new BufferedOutputStream(new FileOutputStream(file));
dsrc.isWriteFile();
dsrc.writeTo(os, null);
os.close();
dsFile = loadDataset(file);
file.delete();
} else {
dsFile = loadDataset(file);
}
return dsFile;
}
private Dataset loadDataset(File file) throws IOException {
BufferedInputStream bis = new BufferedInputStream(new FileInputStream(file));
Dataset ds = factory.newDataset();
try {
ds.readFile(bis, null, -1);
} finally {
try {
bis.close();
} catch (IOException ignore) {
}
}
if (log.isDebugEnabled()) log.debug("Dataset for file " + file + " :" + ds);
return ds;
}
/**
* @param ds
* @param outFile
* @return
* @throws IOException
*/
private RIDResponseObject handleSVG(Dataset ds, BaseDocument doc) throws IOException {
OutputStream out = doc.getOutputStream();
try {
DcmElement elem = ds.get(Tags.WaveformSeq);
WaveformGroup wfgrp =
new WaveformGroup(
ds.getString(Tags.SOPClassUID),
elem,
0,
ridSupport.getWaveformCorrection()); // TODO all groups
if (log.isDebugEnabled()) log.debug(wfgrp);
WaveformInfo wfInfo = new WaveformInfo(ds);
SVGCreator svgCreator = new SVGCreator(wfgrp, wfInfo, new Float(27.6f), new Float(20.3f));
svgCreator.toXML(out);
out.close();
return new RIDStreamResponseObjectImpl(
doc.getInputStream(), CONTENT_TYPE_SVGXML, HttpServletResponse.SC_OK, null);
} catch (Throwable t) {
if (out != null)
try {
out.close();
} catch (IOException e) {
}
log.error("Cant create SVG for Waveform!", t);
log.error("Waveform Dataset:");
log.error(ds);
return new RIDStreamResponseObjectImpl(
null,
RIDSupport.CONTENT_TYPE_HTML,
HttpServletResponse.SC_INTERNAL_SERVER_ERROR,
"Error while creating waveform SVG! Reason:" + t.getMessage());
}
}
private RIDResponseObject handlePDF(Dataset ds, BaseDocument doc) throws IOException {
OutputStream out = doc.getOutputStream();
OutputStream tmpOut = null;
File tmpFile = null;
try {
tmpFile = File.createTempFile("fop_", null);
tmpFile.deleteOnExit();
tmpOut = new FileOutputStream(tmpFile);
DcmElement elem = ds.get(Tags.WaveformSeq);
WaveformGroup[] wfgrps = getWaveformGroups(elem, ds.getString(Tags.SOPClassUID));
WaveformInfo wfInfo = new WaveformInfo(ds);
FOPCreator fopCreator = new FOPCreator(wfgrps, wfInfo, new Float(28.6f), new Float(20.3f));
fopCreator.toXML(tmpOut);
tmpOut.close();
Fop fop = ridSupport.newFop(MimeConstants.MIME_PDF, out);
SAXTransformerFactory tf = (SAXTransformerFactory) TransformerFactory.newInstance();
Transformer t = tf.newTransformer();
t.transform(
new StreamSource(new FileInputStream(tmpFile)), new SAXResult(fop.getDefaultHandler()));
out.close();
tmpFile.delete();
InputStream in = doc.getInputStream();
return new RIDStreamResponseObjectImpl(
in, in.available(), RIDSupport.CONTENT_TYPE_PDF, HttpServletResponse.SC_OK, null);
} catch (Throwable t) {
try {
if (out != null) out.close();
if (tmpOut != null) tmpOut.close();
} catch (IOException e) {
}
if (tmpFile.exists()) tmpFile.delete();
log.error("Cant create PDF for Waveform!", t);
log.error("Waveform Dataset:");
log.error(ds);
return new RIDStreamResponseObjectImpl(
null,
RIDSupport.CONTENT_TYPE_HTML,
HttpServletResponse.SC_INTERNAL_SERVER_ERROR,
"Error while creating waveform PDF! Reason:" + t.getMessage());
}
}
/**
* @param cuid
* @param elem
* @return
*/
private WaveformGroup[] getWaveformGroups(DcmElement elem, String cuid) {
float corr = ridSupport.getWaveformCorrection();
int nrOfWFGroups = elem.countItems();
if (nrOfWFGroups == 1)
return new WaveformGroup[] {new WaveformGroup(cuid, elem, 0, corr)}; // dont
// check
// the
// only
// one
ArrayList l = new ArrayList(nrOfWFGroups);
for (int i = 0; i < nrOfWFGroups; i++) {
try {
l.add(new WaveformGroup(cuid, elem, i, corr));
} catch (Exception x) {
log.warn("Item " + i + " in Waveform Sequence is not valid! Ignored!!");
}
}
return (WaveformGroup[]) l.toArray(new WaveformGroup[l.size()]);
}
}
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;
}
/**
* Queries the archive for DICOM objects matching Attribute Keys defined in the loacal field
* "keys". This field is set by the constructor out of the configuration parameters or by the
* methods setQueryKeys(Configuration) and setQueryKeys(Dataset). See PS 3.4 - Annex C
* QUERY/RETRIEVE SERVICE CLASS.
*
* <p>The method returns, when the result is received from the communication partner.
*
* @return the result of the cFIND as a Vector of Dataset objects each specifying one matching
* DICOM object. If no matching objects are found an empty Vector is returned.
* @throws ConnectException
* @throws IOException
*/
public Vector cFIND() throws ConnectException, IOException, InterruptedException {
List dimseList;
Vector datasetVector;
// An association must be active
if (aassoc == null) {
throw new ConnectException("No Association established");
}
// Test, if Presentation Context for C-FIND is supported
// API doc: Association.getAcceptedPresContext(String asuid, String tsuid)
// UIDs.StudyRootQueryRetrieveInformationModelGET
if ((pc =
aassoc
.getAssociation()
.getAcceptedPresContext(
UIDs.StudyRootQueryRetrieveInformationModelFIND,
UIDs.ExplicitVRLittleEndian))
== null
&& (pc =
aassoc
.getAssociation()
.getAcceptedPresContext(
UIDs.StudyRootQueryRetrieveInformationModelFIND,
UIDs.ImplicitVRLittleEndian))
== null) {
throw new ConnectException(
"Association does not support presentation context for StudyRootQueryRetrieveInformationModelFIND SOP.");
}
// New Cammand Set, see: DICOM Part 7: Message Exchange, 6.3.1 Command Set Structure
Command rqCmd = dof.newCommand();
// API doc: Command.initCFindRQ(int msgID, String sopClassUID, int priority)
rqCmd.initCFindRQ(assoc.nextMsgID(), UIDs.StudyRootQueryRetrieveInformationModelFIND, priority);
// API doc: AssociationFactorynewDimse(int pcid, Command cmd, Dataset ds)
// DIMSE (DICOM Message Service Element) ist ein Nachrichtendienst in DICOM
Dimse findRq = aFact.newDimse(pc.pcid(), rqCmd, keys);
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
FutureRSP future = aassoc.invoke(findRq);
// Response to the C-FIND request.
// The result cannot be accessed until it has been set.
Dimse findRsp = future.get();
// 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());
}
return datasetVector;
}
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 static int maxDiffPixelData(File f1, File f2) throws IOException {
int maxDiff = 0;
InputStream in1 = new BufferedInputStream(new FileInputStream(f1));
try {
InputStream in2 = new BufferedInputStream(new FileInputStream(f2));
try {
DcmObjectFactory df = DcmObjectFactory.getInstance();
DcmParserFactory pf = DcmParserFactory.getInstance();
Dataset attrs1 = df.newDataset();
Dataset attrs2 = df.newDataset();
DcmParser p1 = pf.newDcmParser(in1);
DcmParser p2 = pf.newDcmParser(in2);
p1.setDcmHandler(attrs1.getDcmHandler());
p2.setDcmHandler(attrs2.getDcmHandler());
p1.parseDcmFile(FileFormat.DICOM_FILE, Tags.PixelData);
p2.parseDcmFile(FileFormat.DICOM_FILE, Tags.PixelData);
int samples = attrs1.getInt(Tags.SamplesPerPixel, 1);
int frames = attrs1.getInt(Tags.NumberOfFrames, 1);
int rows = attrs1.getInt(Tags.Rows, 1);
int columns = attrs1.getInt(Tags.Columns, 1);
int bitsAlloc = attrs1.getInt(Tags.BitsAllocated, 8);
int bitsStored = attrs1.getInt(Tags.BitsStored, bitsAlloc);
int bitsStored2 = attrs2.getInt(Tags.BitsStored, bitsAlloc);
int pixelRepresentation1 = attrs1.getInt(Tags.PixelRepresentation, 0);
int pixelRepresentation2 = attrs2.getInt(Tags.PixelRepresentation, 0);
int frameLength = rows * columns * samples * bitsAlloc / 8;
int pixelDataLength = frameLength * frames;
if (pixelDataLength > p1.getReadLength() || pixelDataLength > p2.getReadLength()) {
return Integer.MAX_VALUE;
}
byte[] b1 = new byte[BUFFER_SIZE];
byte[] b2 = new byte[BUFFER_SIZE];
byte lsb1 = 0, lsb2 = 0;
int w1, w2, len, len2;
int bitmask1 = 0xffff >>> (bitsAlloc - bitsStored);
int bitmask2 = 0xffff >>> (bitsAlloc - bitsStored2);
int signed1 = pixelRepresentation1 != 0 ? (-1 & ~bitmask1) >> 1 : 0;
int signed2 = pixelRepresentation2 != 0 ? (-1 & ~bitmask2) >> 1 : 0;
int pos = 0;
while (pos < pixelDataLength) {
len = in1.read(b1, 0, Math.min(pixelDataLength - pos, BUFFER_SIZE));
if (len < 0) // EOF
return Integer.MAX_VALUE;
int off = 0;
while (off < len) {
off += len2 = in2.read(b2, off, len - off);
if (len2 < 0) // EOF
return Integer.MAX_VALUE;
}
if (bitsAlloc == 8)
for (int i = 0; i < len; i++, pos++)
maxDiff = Math.max(maxDiff, Math.abs((b1[i] & 0xff) - (b2[i] & 0xff)));
else {
for (int i = 0; i < len; i++, pos++)
// TODO assumes LE Byte Order
if ((pos & 1) == 0) {
lsb1 = b1[i];
lsb2 = b2[i];
} else {
if (((w1 = ((b1[i] << 8) | (lsb1 & 0xff)) & bitmask1) & signed1) != 0)
w1 |= signed1;
if (((w2 = ((b2[i] << 8) | (lsb2 & 0xff)) & bitmask2) & signed2) != 0)
w2 |= signed2;
maxDiff = Math.max(maxDiff, Math.abs(w1 - w2));
}
}
}
return maxDiff;
} finally {
in2.close();
}
} finally {
in1.close();
}
}
/** * @author [email protected] * @version $Revision: 8056 $ $Date: 2008-11-12 14:31:15 +0100 (Wed, 12 Nov 2008) $ * @since 27.12.2005 * @ejb.bean name="PrivateManager" type="Stateless" view-type="remote" * jndi-name="ejb/PrivateManager" * @ejb.transaction-type type="Container" * @ejb.transaction type="Required" * @ejb.ejb-ref ejb-name="Patient" view-type="local" ref-name="ejb/Patient" * @ejb.ejb-ref ejb-name="Study" view-type="local" ref-name="ejb/Study" * @ejb.ejb-ref ejb-name="Series" view-type="local" ref-name="ejb/Series" * @ejb.ejb-ref ejb-name="Instance" view-type="local" ref-name="ejb/Instance" * @ejb.ejb-ref ejb-name="File" view-type="local" ref-name="ejb/File" * @ejb.ejb-ref ejb-name="PrivatePatient" view-type="local" ref-name="ejb/PrivatePatient" * @ejb.ejb-ref ejb-name="PrivateStudy" view-type="local" ref-name="ejb/PrivateStudy" * @ejb.ejb-ref ejb-name="PrivateSeries" view-type="local" ref-name="ejb/PrivateSeries" * @ejb.ejb-ref ejb-name="PrivateInstance" view-type="local" ref-name="ejb/PrivateInstance" * @ejb.ejb-ref ejb-name="PrivateFile" view-type="local" ref-name="ejb/PrivateFile" */ public abstract class PrivateManagerBean implements SessionBean { private static final int DELETED = 1; private PatientLocalHome patHome; private StudyLocalHome studyHome; private SeriesLocalHome seriesHome; private InstanceLocalHome instHome; private PrivatePatientLocalHome privPatHome; private PrivateStudyLocalHome privStudyHome; private PrivateSeriesLocalHome privSeriesHome; private PrivateInstanceLocalHome privInstHome; private PrivateFileLocalHome privFileHome; private static final DcmObjectFactory dof = DcmObjectFactory.getInstance(); private static Logger log = Logger.getLogger(PrivateManagerBean.class.getName()); public void setSessionContext(SessionContext arg0) throws EJBException, RemoteException { Context jndiCtx = null; try { jndiCtx = new InitialContext(); patHome = (PatientLocalHome) jndiCtx.lookup("java:comp/env/ejb/Patient"); studyHome = (StudyLocalHome) jndiCtx.lookup("java:comp/env/ejb/Study"); seriesHome = (SeriesLocalHome) jndiCtx.lookup("java:comp/env/ejb/Series"); instHome = (InstanceLocalHome) jndiCtx.lookup("java:comp/env/ejb/Instance"); privPatHome = (PrivatePatientLocalHome) jndiCtx.lookup("java:comp/env/ejb/PrivatePatient"); privStudyHome = (PrivateStudyLocalHome) jndiCtx.lookup("java:comp/env/ejb/PrivateStudy"); privSeriesHome = (PrivateSeriesLocalHome) jndiCtx.lookup("java:comp/env/ejb/PrivateSeries"); privInstHome = (PrivateInstanceLocalHome) jndiCtx.lookup("java:comp/env/ejb/PrivateInstance"); privFileHome = (PrivateFileLocalHome) jndiCtx.lookup("java:comp/env/ejb/PrivateFile"); } catch (NamingException e) { throw new EJBException(e); } finally { if (jndiCtx != null) { try { jndiCtx.close(); } catch (NamingException ignore) { } } } } public void unsetSessionContext() { patHome = null; studyHome = null; seriesHome = null; instHome = null; privPatHome = null; privStudyHome = null; privSeriesHome = null; privInstHome = null; privFileHome = null; } /** * @throws FinderException * @ejb.interface-method */ public void deletePrivateSeries(long series_pk) throws RemoteException, FinderException { try { PrivateSeriesLocal series = privSeriesHome.findByPrimaryKey(new Long(series_pk)); PrivateStudyLocal study = series.getStudy(); series.remove(); if (study.getSeries().isEmpty()) { PrivatePatientLocal pat = study.getPatient(); study.remove(); if (pat.getStudies().isEmpty()) { pat.remove(); } } } catch (EJBException e) { throw new RemoteException(e.getMessage()); } catch (RemoveException e) { throw new RemoteException(e.getMessage()); } } /** * @throws FinderException * @ejb.interface-method */ public Collection deletePrivateStudy(long study_pk) throws RemoteException, FinderException { try { PrivateStudyLocal study = privStudyHome.findByPrimaryKey(new Long(study_pk)); ArrayList files = null; PrivatePatientLocal pat = study.getPatient(); study.remove(); if (pat.getStudies().isEmpty()) { pat.remove(); } return files; } catch (EJBException e) { throw new RemoteException(e.getMessage()); } catch (RemoveException e) { throw new RemoteException(e.getMessage()); } } /** @ejb.interface-method */ public void deletePrivatePatient(long patient_pk) throws RemoteException { try { privPatHome.remove(new Long(patient_pk)); } catch (EJBException e) { throw new RemoteException(e.getMessage()); } catch (RemoveException e) { throw new RemoteException(e.getMessage()); } } /** * @throws FinderException * @throws FinderException * @ejb.interface-method */ public void deletePrivateInstance(long instance_pk) throws RemoteException, FinderException { try { PrivateInstanceLocal instance = privInstHome.findByPrimaryKey(new Long(instance_pk)); PrivateSeriesLocal series = instance.getSeries(); instance.remove(); if (series.getInstances().isEmpty()) { PrivateStudyLocal study = series.getStudy(); series.remove(); if (study.getSeries().isEmpty()) { PrivatePatientLocal pat = study.getPatient(); study.remove(); if (pat.getStudies().isEmpty()) { pat.remove(); } } } } catch (EJBException e) { throw new RemoteException(e.getMessage()); } catch (RemoveException e) { throw new RemoteException(e.getMessage()); } } /** * @throws FinderException * @ejb.interface-method */ public void deletePrivateFile(long file_pk) throws RemoteException { try { privFileHome.remove(new Long(file_pk)); } catch (EJBException e) { throw new RemoteException(e.getMessage()); } catch (RemoveException e) { throw new RemoteException(e.getMessage()); } } /** * @throws FinderException * @ejb.interface-method */ public void deletePrivateFiles(Collection fileDTOs) throws RemoteException { try { for (Iterator iter = fileDTOs.iterator(); iter.hasNext(); ) { privFileHome.remove(new Long(((FileDTO) iter.next()).getPk())); } } catch (EJBException e) { throw new RemoteException(e.getMessage()); } catch (RemoveException e) { throw new RemoteException(e.getMessage()); } } /** @ejb.interface-method */ public void deleteAll(int privateType) throws RemoteException { try { Collection c = privPatHome.findByPrivateType(privateType); for (Iterator iter = c.iterator(); iter.hasNext(); ) { privPatHome.remove(((PrivatePatientLocal) iter.next()).getPk()); } } catch (EJBException e) { throw new RemoteException(e.getMessage()); } catch (RemoveException e) { throw new RemoteException(e.getMessage()); } catch (FinderException e) { throw new RemoteException(e.getMessage()); } } /** * Delete a list of instances, i.e., move them to trash bin * * @ejb.interface-method * @param iuids A list of instance uid * @param cascading True to delete the series/study if there's no instance/series * @return a collection of Dataset containing the actuall detetion information per study * @throws RemoteException */ public Collection moveInstancesToTrash(String[] iuids, boolean cascading) throws RemoteException { try { // These instances may belong to multiple studies, // although mostly they should be the same study Map mapStudies = new HashMap(); for (int i = 0; i < iuids.length; i++) { InstanceLocal instance = instHome.findBySopIuid(iuids[i]); SeriesLocal series = instance.getSeries(); StudyLocal study = series.getStudy(); if (!mapStudies.containsKey(study)) mapStudies.put(study, new HashMap()); Map mapSeries = (Map) mapStudies.get(study); if (!mapSeries.containsKey(series)) mapSeries.put(series, new ArrayList()); Collection colInstances = (Collection) mapSeries.get(series); colInstances.add(instance); } List dss = new ArrayList(); Iterator iter = mapStudies.keySet().iterator(); while (iter.hasNext()) { StudyLocal study = (StudyLocal) iter.next(); dss.add(getStudyMgtDataset(study, (Map) mapStudies.get(study))); Iterator iter2 = ((Map) mapStudies.get(study)).keySet().iterator(); while (iter2.hasNext()) { SeriesLocal series = (SeriesLocal) iter2.next(); List instances = (List) ((Map) mapStudies.get(study)).get(series); for (int i = 0; i < instances.size(); i++) { // Delete the instance now, i.e., move to trash bin, // becoming private instance getPrivateInstance((InstanceLocal) instances.get(i), DELETED, null); ((InstanceLocal) instances.get(i)).remove(); } if (series.getInstances().size() == 0 && cascading) { // Delete the series too since there's no instance left getPrivateSeries(series, DELETED, null, false); series.remove(); } else UpdateDerivedFieldsUtils.updateDerivedFieldsOf(series); } if (study.getSeries().size() == 0 && cascading) { // Delete the study too since there's no series left getPrivateStudy(study, DELETED, null, false); study.remove(); } else UpdateDerivedFieldsUtils.updateDerivedFieldsOf(study); } return dss; } catch (CreateException e) { throw new RemoteException(e.getMessage()); } catch (EJBException e) { throw new RemoteException(e.getMessage()); } catch (FinderException e) { throw new RemoteException(e.getMessage()); } catch (RemoveException e) { throw new RemoteException(e.getMessage()); } } /** @ejb.interface-method */ public Dataset moveInstanceToTrash(long instance_pk) throws RemoteException { try { InstanceLocal instance = instHome.findByPrimaryKey(new Long(instance_pk)); Collection colInstance = new ArrayList(); colInstance.add(instance); SeriesLocal series = instance.getSeries(); Map mapSeries = new HashMap(); mapSeries.put(series, colInstance); Dataset ds = getStudyMgtDataset(series.getStudy(), mapSeries); getPrivateInstance(instance, DELETED, null); instance.remove(); UpdateDerivedFieldsUtils.updateDerivedFieldsOf(series); UpdateDerivedFieldsUtils.updateDerivedFieldsOf(series.getStudy()); return ds; } catch (CreateException e) { throw new RemoteException(e.getMessage()); } catch (EJBException e) { throw new RemoteException(e.getMessage()); } catch (FinderException e) { throw new RemoteException(e.getMessage()); } catch (RemoveException e) { throw new RemoteException(e.getMessage()); } } /** @ejb.interface-method */ public Dataset moveSeriesToTrash(long series_pk) throws RemoteException { try { SeriesLocal series = seriesHome.findByPrimaryKey(new Long(series_pk)); StudyLocal study = series.getStudy(); Map mapSeries = new HashMap(); mapSeries.put(series, series.getInstances()); Dataset ds = getStudyMgtDataset(series.getStudy(), mapSeries); getPrivateSeries(series, DELETED, null, true); series.remove(); UpdateDerivedFieldsUtils.updateDerivedFieldsOf(study); return ds; } catch (CreateException e) { throw new RemoteException(e.getMessage()); } catch (EJBException e) { throw new RemoteException(e.getMessage()); } catch (FinderException e) { throw new RemoteException(e.getMessage()); } catch (RemoveException e) { throw new RemoteException(e.getMessage()); } } /** @ejb.interface-method */ public Collection moveSeriesOfPPSToTrash(String ppsIUID, boolean removeEmptyParents) throws RemoteException { Collection result = new ArrayList(); // FIXME: NOT IN USE try { Object[] ppsSeries = seriesHome.findByPpsIuid(ppsIUID).toArray(); if (ppsSeries.length > 0) { SeriesLocal series = null; StudyLocal study = ((SeriesLocal) ppsSeries[0]).getStudy(); for (int i = 0; i < ppsSeries.length; i++) { series = (SeriesLocal) ppsSeries[i]; getPrivateSeries(series, DELETED, null, true); series.remove(); } if (removeEmptyParents && study.getSeries().isEmpty()) { study.remove(); } else { UpdateDerivedFieldsUtils.updateDerivedFieldsOf(study); } } } catch (FinderException ignore) { } catch (Exception e) { throw new RemoteException(e.getMessage()); } return result; } /** @ejb.interface-method */ public Dataset moveStudyToTrash(String iuid) throws RemoteException { try { StudyLocal study = studyHome.findByStudyIuid(iuid); if (study != null) return moveStudyToTrash(study.getPk().longValue()); else return null; } catch (EJBException e) { throw new RemoteException(e.getMessage()); } catch (FinderException e) { throw new RemoteException(e.getMessage()); } } /** @ejb.interface-method */ public Dataset moveStudyToTrash(long study_pk) throws RemoteException { try { StudyLocal study = studyHome.findByPrimaryKey(new Long(study_pk)); Dataset ds = getStudyMgtDataset(study, null); getPrivateStudy(study, DELETED, null, true); study.remove(); return ds; } catch (CreateException e) { throw new RemoteException(e.getMessage()); } catch (EJBException e) { throw new RemoteException(e.getMessage()); } catch (FinderException e) { throw new RemoteException(e.getMessage()); } catch (RemoveException e) { throw new RemoteException(e.getMessage()); } } /** @ejb.interface-method */ public Collection movePatientToTrash(long pat_pk) throws RemoteException { try { PatientLocal patient = patHome.findByPrimaryKey(new Long(pat_pk)); Collection col = patient.getStudies(); Collection result = new ArrayList(); for (Iterator iter = col.iterator(); iter.hasNext(); ) { result.add(getStudyMgtDataset((StudyLocal) iter.next(), null)); } Dataset ds = patient.getAttributes(true); getPrivatePatient(patient, DELETED, true); patient.remove(); if (result.isEmpty()) result.add(ds); return result; } catch (CreateException e) { throw new RemoteException(e.getMessage()); } catch (EJBException e) { throw new RemoteException(e.getMessage()); } catch (FinderException e) { throw new RemoteException(e.getMessage()); } catch (RemoveException e) { throw new RemoteException(e.getMessage()); } } private PrivateInstanceLocal getPrivateInstance( InstanceLocal instance, int type, PrivateSeriesLocal privSeries) throws FinderException, CreateException { Collection col = privInstHome.findBySopIuid(type, instance.getSopIuid()); PrivateInstanceLocal privInstance; if (col.isEmpty()) { if (privSeries == null) { privSeries = getPrivateSeries(instance.getSeries(), type, null, false); } privInstance = privInstHome.create(type, instance.getAttributes(true), privSeries); } else { privInstance = (PrivateInstanceLocal) col.iterator().next(); } Object[] files = instance.getFiles().toArray(); FileLocal file; for (int i = 0; i < files.length; i++) { file = (FileLocal) files[i]; privFileHome.create( file.getFilePath(), file.getFileTsuid(), file.getFileSize(), file.getFileMd5(), file.getFileStatus(), privInstance, file.getFileSystem()); try { file.remove(); } catch (Exception x) { log.warn("Can not remove File record:" + file, x); } } return privInstance; } private PrivateSeriesLocal getPrivateSeries( SeriesLocal series, int type, PrivateStudyLocal privStudy, boolean includeInstances) throws FinderException, CreateException { Collection col = privSeriesHome.findBySeriesIuid(type, series.getSeriesIuid()); PrivateSeriesLocal privSeries; if (col.isEmpty()) { if (privStudy == null) { privStudy = getPrivateStudy(series.getStudy(), type, null, false); } privSeries = privSeriesHome.create(type, series.getAttributes(true), privStudy); } else { privSeries = (PrivateSeriesLocal) col.iterator().next(); } if (includeInstances) { for (Iterator iter = series.getInstances().iterator(); iter.hasNext(); ) { getPrivateInstance( (InstanceLocal) iter.next(), type, privSeries); // move also all instances } } return privSeries; } private PrivateStudyLocal getPrivateStudy( StudyLocal study, int type, PrivatePatientLocal privPat, boolean includeSeries) throws FinderException, CreateException { Collection col = privStudyHome.findByStudyIuid(type, study.getStudyIuid()); PrivateStudyLocal privStudy; if (col.isEmpty()) { if (privPat == null) { privPat = getPrivatePatient(study.getPatient(), type, false); } privStudy = privStudyHome.create(type, study.getAttributes(true), privPat); } else { privStudy = (PrivateStudyLocal) col.iterator().next(); } if (includeSeries) { for (Iterator iter = study.getSeries().iterator(); iter.hasNext(); ) { getPrivateSeries( (SeriesLocal) iter.next(), type, privStudy, true); // move also all instances } } return privStudy; } private PrivatePatientLocal getPrivatePatient( PatientLocal patient, int type, boolean includeStudies) throws FinderException, CreateException { Collection col = privPatHome.findByPatientIdWithIssuer( type, patient.getPatientId(), patient.getIssuerOfPatientId()); PrivatePatientLocal privPat; if (col.isEmpty()) { privPat = privPatHome.create(type, patient.getAttributes(true)); } else { privPat = (PrivatePatientLocal) col.iterator().next(); } if (includeStudies) { for (Iterator iter = patient.getStudies().iterator(); iter.hasNext(); ) { getPrivateStudy((StudyLocal) iter.next(), type, privPat, true); // move // also // all // instances } } return privPat; } private Dataset getStudyMgtDataset(StudyLocal study, Map mapSeries) { Dataset ds = dof.newDataset(); ds.putUI(Tags.StudyInstanceUID, study.getStudyIuid()); ds.putOB(PrivateTags.StudyPk, Convert.toBytes(study.getPk().longValue())); ds.putSH(Tags.AccessionNumber, study.getAccessionNumber()); ds.putLO(Tags.PatientID, study.getPatient().getPatientId()); ds.putLO(Tags.IssuerOfPatientID, study.getPatient().getIssuerOfPatientId()); ds.putPN(Tags.PatientName, study.getPatient().getPatientName()); log.debug("getStudyMgtDataset: studyIUID:" + study.getStudyIuid()); DcmElement refSeriesSeq = ds.putSQ(Tags.RefSeriesSeq); Iterator iter = (mapSeries == null) ? study.getSeries().iterator() : mapSeries.keySet().iterator(); while (iter.hasNext()) { SeriesLocal sl = (SeriesLocal) iter.next(); Dataset dsSer = refSeriesSeq.addNewItem(); dsSer.putUI(Tags.SeriesInstanceUID, sl.getSeriesIuid()); Collection instances = (mapSeries == null) ? sl.getInstances() : (Collection) mapSeries.get(sl); Iterator iter2 = instances.iterator(); DcmElement refSopSeq = null; if (iter2.hasNext()) refSopSeq = dsSer.putSQ(Tags.RefSOPSeq); while (iter2.hasNext()) { InstanceLocal il = (InstanceLocal) iter2.next(); Dataset dsInst = refSopSeq.addNewItem(); dsInst.putUI(Tags.RefSOPClassUID, il.getSopCuid()); dsInst.putUI(Tags.RefSOPInstanceUID, il.getSopIuid()); dsInst.putAE(Tags.RetrieveAET, il.getRetrieveAETs()); } } if (log.isDebugEnabled()) { log.debug("return StgMgtDataset:"); log.debug(ds); } return ds; } }