private void emitReferencedValue(AttributeList attrs) throws SAXException {
if (expectingTarget) {
String previousElement = "";
if (!elementStack.empty()) {
previousElement = (String) elementStack.peek();
}
int prevSrxId = XmiMapping.getSrxId(previousElement);
// enabledOutput = toProcess(prevSrxId);
if (!enabledOutput) {
return;
}
if (attrs != null) {
for (int i = 0; i < attrs.getLength(); i++) {
String attr = attrs.getName(i);
if (attr.equals(kTarget)) {
String key = attrs.getValue(i);
String name = (String) idTable.get(key);
if (name != null) {
emit(name + eol);
}
expectingTarget = false;
}
} // end for
} // end if
} // end if
} // end emitReferencedValue()
public void startElement(String name, AttributeList atts)
throws org.xml.sax.SAXException
{
//-- strip namespace prefix
int idx = name.indexOf(':');
if (idx >= 0) {
name = name.substring(idx+1);
}
StateInfo sInfo = null;
boolean topLevel = false;
//-- if we are currently in another element
//-- definition...flag as complex content
if (!_siStack.isEmpty()) {
sInfo = (StateInfo)_siStack.peek();
sInfo.complex = true;
}
else {
topLevel = true;
}
//-- create current holder for stateInformation
sInfo = new StateInfo();
sInfo.topLevel = topLevel;
_siStack.push(sInfo);
//-- create element definition
sInfo.element = new ElementDecl(_schema, name);
//-- create attributes
for (int i = 0; i < atts.getLength(); i++) {
String attName = atts.getName(i);
//-- skip namespace declarations
if (attName.equals(XMLNS)) continue;
String prefix = "";
idx = attName.indexOf(':');
if (idx >= 0) {
prefix = attName.substring(0, idx);
attName = attName.substring(idx+1);
}
if (prefix.equals(XMLNS)) continue;
AttributeDecl attr = new AttributeDecl(_schema, attName);
//-- guess simple type
String typeName = _nsPrefix + ':' +
DatatypeHandler.guessType(atts.getValue(i));
attr.setSimpleTypeReference(typeName);
sInfo.attributes.addElement(attr);
}
} //-- startElement
/**
* Read a DICOM dataset and write an XML representation of it to the standard output, or vice
* versa.
*
* @param arg either one filename of the file containing the DICOM dataset, or a direction
* argument (toDICOM or toXML, case insensitive) and an input filename
*/
public static void main(String arg[]) {
try {
boolean bad = true;
boolean toXML = true;
String filename = null;
if (arg.length == 1) {
bad = false;
toXML = true;
filename = arg[0];
} else if (arg.length == 2) {
filename = arg[1];
if (arg[0].toLowerCase(java.util.Locale.US).equals("toxml")) {
bad = false;
toXML = true;
} else if (arg[0].toLowerCase(java.util.Locale.US).equals("todicom")
|| arg[0].toLowerCase(java.util.Locale.US).equals("todcm")) {
bad = false;
toXML = false;
}
}
if (bad) {
System.err.println(
"usage: XMLRepresentationOfDicomObjectFactory [toDICOM|toXML] inputfile");
} else {
if (toXML) {
AttributeList list = new AttributeList();
// System.err.println("reading list");
list.read(filename, null, true, true);
// System.err.println("making document");
Document document = new XMLRepresentationOfDicomObjectFactory().getDocument(list);
// System.err.println(toString(document));
write(System.out, document);
} else {
// long startReadTime = System.currentTimeMillis();
AttributeList list =
new XMLRepresentationOfDicomObjectFactory().getAttributeList(filename);
// System.err.println("AttributeList.main(): read XML and create DICOM AttributeList -
// done in "+(System.currentTimeMillis()-startReadTime)+" ms");
String sourceApplicationEntityTitle =
Attribute.getSingleStringValueOrEmptyString(
list, TagFromName.SourceApplicationEntityTitle);
list.removeMetaInformationHeaderAttributes();
FileMetaInformation.addFileMetaInformation(
list, TransferSyntax.ExplicitVRLittleEndian, sourceApplicationEntityTitle);
list.write(
System.out,
TransferSyntax.ExplicitVRLittleEndian,
true /*useMeta*/,
true /*useBufferedStream*/);
}
}
} catch (Exception e) {
e.printStackTrace(System.err);
}
}
public void TestSafePrivateGEPACSRelated_CreatorFromList() throws Exception {
AttributeList list = new AttributeList();
{
Attribute a = new LongStringAttribute(new AttributeTag(0x0903, 0x0010));
a.addValue("GEIIS PACS");
list.put(a);
}
assertTrue(
"Checking Reject Image Flag is safe",
ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0903, 0x1010), list));
}
/**
* This method is called for the end tag of the root document tag. If there are name spaces, they
* would have been defined in this tag. Insert them in the front of the attribute list.
*
* @throws XmlPullParserException
*/
private void addNamespaces(int depth) throws XmlPullParserException {
TagNode tag = (TagNode) mDocumentTag;
AttributeList attrList = tag.getAttrList();
int nsStart = mParser.getNamespaceCount(depth - 1);
int nsEnd = mParser.getNamespaceCount(depth);
for (int i = nsEnd - 1; i >= nsStart; i--) {
Attribute attr = buildNS(i);
attrList.insert(attr);
}
} // addNamespaces
/* ------------------------------------------------------------ */
public AttributeList getAttributes(String[] names) {
log.debug("getAttributes");
AttributeList results = new AttributeList(names.length);
for (int i = 0; i < names.length; i++) {
try {
results.add(new Attribute(names[i], getAttribute(names[i])));
} catch (Exception e) {
log.warn(LogSupport.EXCEPTION, e);
}
}
return results;
}
private AttributeList getAttributes(ObjectName objName, String[] attrNames)
throws InstanceNotFoundException, ReflectionException, IOException {
final NameValueMap values =
getCachedAttributes(objName, new TreeSet<String>(Arrays.asList(attrNames)));
final AttributeList list = new AttributeList();
for (String attrName : attrNames) {
final Object value = values.get(attrName);
if (value != null || values.containsKey(attrName)) {
list.add(new Attribute(attrName, value));
}
}
return list;
}
public void TestSafePrivatePhilipsPETRelated_ScaleFactors_FromList() throws Exception {
AttributeList list = new AttributeList();
{
Attribute a = new LongStringAttribute(new AttributeTag(0x7053, 0x0010));
a.addValue("Philips PET Private Group");
list.put(a);
}
assertTrue(
"Checking SUV Factor is safe",
ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x7053, 0x1000), list));
assertTrue(
"Checking Activity Concentration Factor is safe",
ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x7053, 0x1009), list));
}
public void TestSafePrivateGEPACSRelated_FromFile() throws Exception {
AttributeList list = new AttributeList();
String testFilePath = System.getProperty("com.pixelmed.test.filepath");
// System.err.println("TestSafePrivateGEPACSRelated.TestSafePrivateGEPACSRelated_FromFile():
// testFilePath = "+testFilePath);
list.read(new java.io.File(testFilePath, "philipsctwithgepacsprivateattributes.dcm"));
// System.err.print("TestSafePrivateGEPACSRelated.TestSafePrivateGEPACSRelated():\n"+list);
list.removeUnsafePrivateAttributes();
assertTrue(
"Checking Creator is not removed", list.get(new AttributeTag(0x0903, 0x0010)) != null);
assertTrue(
"Checking Reject Image Flag is not removed",
list.get(new AttributeTag(0x0903, 0x1010)) != null);
}
private static boolean checkAttrs(String what, AttributeList attrs) {
if (attrs.size() != 1) {
System.out.println(
"TEST FAILS: list returned by " + what + " does not have size 1: " + attrs);
return false;
}
Attribute attr = (Attribute) attrs.get(0);
if (!"Exotic".equals(attr.getName())) {
System.out.println("TEST FAILS: " + what + " returned wrong " + "attribute: " + attr);
return false;
}
return true;
}
/**
* Build a tag node. Note that a tag node always has an AttributeList object, even if there is no
* attribute list. This wastes some memory, but in theory should make the tree processing more
* regular, since it can always be assumed that this object exits.
*/
private TagNode buildTagNode() {
String name = mParser.getName();
// String prefix = mParser.getPrefix();
String prefix = null;
String namespace = mParser.getNamespace();
TagNode tag = new TagNode(name, prefix, namespace);
AttributeList attrList = new AttributeList();
int numAttr = mParser.getAttributeCount();
for (int i = 0; i < numAttr; i++) {
Attribute attr = buildAttr(i);
attrList.append(attr);
} // for
tag.setAttrList(attrList);
return tag;
} // buildTagNode
/* ------------------------------------------------------------ */
public AttributeList setAttributes(AttributeList attrs) {
log.debug("setAttributes");
AttributeList results = new AttributeList(attrs.size());
Iterator iter = attrs.iterator();
while (iter.hasNext()) {
try {
Attribute attr = (Attribute) iter.next();
setAttribute(attr);
results.add(new Attribute(attr.getName(), getAttribute(attr.getName())));
} catch (Exception e) {
log.warn(LogSupport.EXCEPTION, e);
}
}
return results;
}
public void writeClass(OutputStream is) throws IOException {
DataOutputStream classStream = new DataOutputStream(is);
classStream.writeInt(magic);
classStream.writeShort(minorVersion);
classStream.writeShort(majorVersion);
classStream.writeShort(constantPool.size());
Iterator<CPInfo> i = constantPool.iterator();
i.next(); // Skip initial, not really there entry
for (; i.hasNext(); ) {
CPInfo poolEntry = i.next();
poolEntry.write(classStream);
// Constant pool array must have null entry after long or double
if (poolEntry.tag == CONSTANT_Double || poolEntry.tag == CONSTANT_Long) i.next();
}
classStream.writeShort(accessFlags);
classStream.writeShort(thisClassIndex);
classStream.writeShort(superClassIndex);
classStream.writeShort(interfaces.size());
for (Iterator<Integer> j = interfaces.iterator(); j.hasNext(); ) {
classStream.writeShort(j.next());
}
classStream.writeShort(fields.size());
for (Iterator<FieldInfo> j = fields.iterator(); j.hasNext(); ) {
j.next().write(classStream);
}
classStream.writeShort(methods.size());
for (Iterator<MethodInfo> j = methods.iterator(); j.hasNext(); ) {
j.next().write(classStream);
}
attributes.write(classStream);
}
CreateCommand(UnicoreInvokeServer is, String requestId) throws Command.Exception {
super(is);
this.requestId = requestId;
String line;
while ((line = is.readLine()) != null) {
if (line.trim().equals(CMD_CREATE_END)) {
terminated = true;
break;
} else {
try {
StringTokenizer st = new StringTokenizer(line);
String key = st.nextToken();
String value = line.substring(key.length());
list.put(key, value);
} catch (java.lang.Exception e) {
Log.printStackTrace(e);
}
}
}
if (terminated) {
job = new UnicoreJob(this);
} else {
new Command.Exception("the command was not terminated!");
}
}
public List<org.openprovenance.prov.model.Other> getOther() {
if (others == null) {
others =
AttributeList.populateKnownAttributes(
this, all, org.openprovenance.prov.model.Other.class);
}
return this.others;
}
/**
* Gets the value of the type property.
*
* <p>This accessor method returns a reference to the live list, not a snapshot. Therefore any
* modification you make to the returned list will be present inside the JAXB object. This is why
* there is not a <CODE>set</CODE> method for the type property.
*
* <p>For example, to add a new item, do as follows:
*
* <pre>
* getType().add(newItem);
* </pre>
*
* <p>Objects of the following type(s) are allowed in the list {@link
* org.openprovenance.prov.xml.Type }
*/
public List<org.openprovenance.prov.model.Type> getType() {
if (type == null) {
type =
AttributeList.populateKnownAttributes(
this, all, org.openprovenance.prov.model.Type.class);
}
return this.type;
}
/**
* Gets the value of the role property.
*
* <p>This accessor method returns a reference to the live list, not a snapshot. Therefore any
* modification you make to the returned list will be present inside the JAXB object. This is why
* there is not a <CODE>set</CODE> method for the role property.
*
* <p>For example, to add a new item, do as follows:
*
* <pre>
* getRole().add(newItem);
* </pre>
*
* <p>Objects of the following type(s) are allowed in the list {@link
* org.openprovenance.prov.xml.Role }
*/
public List<org.openprovenance.prov.model.Role> getRole() {
if (role == null) {
role =
AttributeList.populateKnownAttributes(
this, all, org.openprovenance.prov.model.Role.class);
}
return this.role;
}
void commit() {
if (attList == null || !attList.hasOption("autowidth")) {
double width = 100.0 / count;
ColumnContext col = rootColumn;
for (int i = 0; i < count; i++) {
col.width = width;
col = col.next;
}
}
}
/**
* Creates a new AppInfoUnmarshaller
*
* @param atts the AttributeList
*/
public AppInfoUnmarshaller(AttributeList atts) throws SAXException {
super();
_appInfo = new AppInfo();
// -- handle attributes
String attValue = null;
_appInfo.setSource(atts.getValue(SchemaNames.BASE_ATTR));
} // -- AppInfoUnmarshaller
public void TestSafePrivateGEPACSRelated_AddedToList() throws Exception {
AttributeList list = new AttributeList();
{
Attribute a = new LongStringAttribute(new AttributeTag(0x0903, 0x0010));
a.addValue("GEIIS PACS");
list.put(a);
}
{
Attribute a = new UnsignedShortAttribute(new AttributeTag(0x0903, 0x1010));
a.addValue(0);
list.put(a);
}
list.removeUnsafePrivateAttributes();
assertTrue(
"Checking Creator is not removed", list.get(new AttributeTag(0x0903, 0x0010)) != null);
assertTrue(
"Checking Reject Image Flag is not removed",
ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0903, 0x1010), list));
}
/**
* @exception IOException
* @exception DicomException
*/
public CEchoRequestCommandMessage() throws DicomException, IOException {
commandField = MessageServiceElementCommand.C_ECHO_RQ;
messageID = super.getNextAvailableMessageID();
int dataSetType = 0x0101; // none
// NB. The Affected SOP Class UID should have no extra trailing padding, otherwise the
// SCP may fail and send an A-ABORT :) (Part 5 says one null (not space) is allowed)
// This is taken care of by the Attribute.write()
AttributeList list = new AttributeList();
{
AttributeTag t = groupLengthTag;
Attribute a = new UnsignedLongAttribute(t);
a.addValue(0);
list.put(t, a);
}
{
AttributeTag t = TagFromName.AffectedSOPClassUID;
Attribute a = new UniqueIdentifierAttribute(t);
a.addValue(SOPClass.Verification);
list.put(t, a);
}
{
AttributeTag t = TagFromName.CommandField;
Attribute a = new UnsignedShortAttribute(t);
a.addValue(commandField);
list.put(t, a);
}
{
AttributeTag t = TagFromName.MessageID;
Attribute a = new UnsignedShortAttribute(t);
a.addValue(messageID);
list.put(t, a);
}
{
AttributeTag t = TagFromName.CommandDataSetType;
Attribute a = new UnsignedShortAttribute(t);
a.addValue(dataSetType);
list.put(t, a);
}
ByteArrayOutputStream bout = new ByteArrayOutputStream();
DicomOutputStream dout =
new DicomOutputStream(
bout, null /* no meta-header */, TransferSyntax.ImplicitVRLittleEndian);
list.write(dout);
bytes = bout.toByteArray();
groupLength = bytes.length - 12;
bytes[8] = (byte) groupLength; // little endian
bytes[9] = (byte) (groupLength >> 8);
bytes[10] = (byte) (groupLength >> 16);
bytes[11] = (byte) (groupLength >> 24);
// System.err.println("CEchoRequestCommandMessage: bytes="+HexDump.dump(bytes));
}
private synchronized NameValueMap getCachedAttributes(ObjectName objName, Set<String> attrNames)
throws InstanceNotFoundException, ReflectionException, IOException {
NameValueMap values = cachedValues.get(objName);
if (values != null && values.keySet().containsAll(attrNames)) {
return values;
}
attrNames = new TreeSet<String>(attrNames);
Set<String> oldNames = cachedNames.get(objName);
if (oldNames != null) {
attrNames.addAll(oldNames);
}
values = new NameValueMap();
final AttributeList attrs =
conn.getAttributes(objName, attrNames.toArray(new String[attrNames.size()]));
for (Attribute attr : attrs.asList()) {
values.put(attr.getName(), attr.getValue());
}
cachedValues.put(objName, values);
cachedNames.put(objName, attrNames);
return values;
}
public void TestSafePrivateGEMRRelated_CreatorFromList() throws Exception {
{
AttributeList list = new AttributeList();
{
Attribute a = new LongStringAttribute(new AttributeTag(0x0019, 0x0010));
a.addValue("GEMS_ACQU_01");
list.put(a);
}
assertTrue(
"Internal Pulse Sequence Name is safe",
ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0019, 0x109E), list));
}
{
AttributeList list = new AttributeList();
{
Attribute a = new LongStringAttribute(new AttributeTag(0x0025, 0x0010));
a.addValue("GEMS_SERS_01");
list.put(a);
}
assertTrue(
"Images In Series is safe",
ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0025, 0x1007), list));
}
{
AttributeList list = new AttributeList();
{
Attribute a = new LongStringAttribute(new AttributeTag(0x0043, 0x0010));
a.addValue("GEMS_PARM_01");
list.put(a);
}
assertTrue(
"Scanner Table Entry + Gradient Coil Selected",
ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0043, 0x106F), list));
}
}
private void testIsNotRemovedAndRetainsValue(
String description,
AttributeTag creatorTag,
String creator,
Attribute privateAttribute,
String expectValue)
throws DicomException {
AttributeList list = new AttributeList();
{
Attribute a = new LongStringAttribute(creatorTag);
a.addValue(creator);
list.put(a);
}
list.put(privateAttribute);
AttributeTag privateTag = privateAttribute.getTag();
list.removeUnsafePrivateAttributes();
assertTrue("Checking Creator is not removed", list.get(creatorTag) != null);
assertEquals(
"Checking Creator retains value",
creator,
Attribute.getDelimitedStringValuesOrEmptyString(list, creatorTag));
assertTrue("Checking " + description + " is not removed", list.get(privateTag) != null);
assertEquals(
"Checking " + description + " retains value",
expectValue,
Attribute.getDelimitedStringValuesOrEmptyString(list, privateTag));
}
public String getSourceFile() {
SourceFileAttribute sfa =
(SourceFileAttribute) attributes.getAttributeByType(SourceFileAttribute.typeString);
if (sfa != null) {
return sfa.getSourceFile();
}
String internalName = getInternalClassName(getCurrentClassIndex());
int lastSlash = internalName.lastIndexOf('/');
if (lastSlash != -1) internalName = internalName.substring(lastSlash + 1);
int firstPeriod = internalName.indexOf('$');
if (firstPeriod != -1) internalName = internalName.substring(0, firstPeriod);
return internalName + ".java";
}
private void emitNewOccurrence(int srxId, AttributeList attrs) throws SAXException {
enabledOutput = toProcess(srxId);
if (!enabledOutput) {
return;
}
currentSrxId = srxId;
String mappedName = XmiMapping.getMappingName(srxId);
emit(eol + kOccurrenceType + " " + mappedName + eol);
// if it's a component, write its composite
String composite = XmiMapping.getComposite(srxId);
if (composite != null) {
if (!occurrenceNameStack.empty()) {
String compositeName = (String) occurrenceNameStack.peek();
if (compositeName != null) {
emit(composite + " " + compositeName + eol);
}
} // end if
} // end if
// Keep its XMI.id
if (attrs != null) {
for (int i = 0; i < attrs.getLength(); i++) {
String attr = attrs.getName(i);
if (attr.equals(kXmiId)) {
currentXmiId = attrs.getValue(i);
} // end if
} // end for
} // end if
// Keep its current XMI name & SRX name
currentXmiName = XmiMapping.getXmiName(srxId);
currentSrxName = XmiMapping.getSrxName(srxId);
}
/**
* @param list
* @return array of two String values, row then column orientation, else array of two nulls if
* cannot be obtained
*/
private static String[] getPatientOrientation(AttributeList list) {
String[] vPatientOrientation = null;
Attribute aPatientOrientation = list.get(TagFromName.PatientOrientation);
if (aPatientOrientation != null && aPatientOrientation.getVM() == 2) {
try {
vPatientOrientation = aPatientOrientation.getStringValues();
if (vPatientOrientation != null && vPatientOrientation.length != 2) {
vPatientOrientation = null;
}
} catch (DicomException e) {
vPatientOrientation = null;
}
}
if (vPatientOrientation == null) {
vPatientOrientation = new String[2];
}
return vPatientOrientation;
}
public void TestSafePrivatePhilipsPETRelated_ScaleFactors_FromFile() throws Exception {
AttributeList list = new AttributeList();
String testFilePath = System.getProperty("com.pixelmed.test.filepath");
// System.err.println("TestSafePrivatePhilipsPETRelated.TestSafePrivatePhilipsPETRelated_ScaleFactors_FromFile(): testFilePath = "+testFilePath);
list.read(new java.io.File(testFilePath, "philipssuvandactivityscalefactors.dcm"));
// System.err.print("TestSafePrivatePhilipsPETRelated.TestSafePrivatePhilipsPETRelated_ScaleFactors():\n"+list);
list.removeUnsafePrivateAttributes();
assertTrue(
"Checking Creator is not removed", list.get(new AttributeTag(0x7053, 0x0010)) != null);
assertTrue(
"Checking SUV Factor is not removed", list.get(new AttributeTag(0x7053, 0x1000)) != null);
assertTrue(
"Checking Activity Concentration Factor is not removed",
list.get(new AttributeTag(0x7053, 0x1009)) != null);
}
public void readClass(InputStream is) throws IOException, CodeCheckException {
clearClass();
DataInputStream classStream = new DataInputStream(is);
magic = classStream.readInt();
minorVersion = classStream.readUnsignedShort();
majorVersion = classStream.readUnsignedShort();
constantPool.add(null);
int constantPoolCount = classStream.readUnsignedShort();
int i;
for (i = 1; i < constantPoolCount; i++) {
CPInfo poolEntry = readConstant(classStream);
constantPool.add(poolEntry);
if (poolEntry.tag == CONSTANT_Double || poolEntry.tag == CONSTANT_Long) {
i++;
constantPool.add(null);
}
}
accessFlags = classStream.readUnsignedShort();
thisClassIndex = classStream.readUnsignedShort();
superClassIndex = classStream.readUnsignedShort();
int interfacesCount = classStream.readUnsignedShort();
for (i = 0; i < interfacesCount; i++) {
interfaces.add(new Integer(classStream.readUnsignedShort()));
}
int fieldsCount = classStream.readUnsignedShort();
for (i = 0; i < fieldsCount; i++) {
fields.add(readFieldInfo(classStream));
}
int methodsCount = classStream.readUnsignedShort();
for (i = 0; i < methodsCount; i++) {
methods.add(readMethodInfo(classStream));
}
attributes.read(classStream);
}
/**
* Generate commomn attributes for converted images.
*
* <p>Does NOT add ManufacturerModelName ... that should be added by caller.
*
* <p>Does NOT call
* CodingSchemeIdentification.replaceCodingSchemeIdentificationSequenceWithCodingSchemesUsedInAttributeList
* ... that should be done by caller.
*
* @param list
* @param patientName
* @param patientID
* @param studyID
* @param seriesNumber
* @param instanceNumber
* @param modality may be null
* @param sopClass may be null
* @throws DicomException
* @throws NumberFormatException
*/
public static void generateCommonAttributes(
AttributeList list,
String patientName,
String patientID,
String studyID,
String seriesNumber,
String instanceNumber,
String modality,
String sopClass)
throws DicomException {
UIDGenerator u = new UIDGenerator();
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.SOPInstanceUID);
a.addValue(u.getAnotherNewUID());
list.put(a);
}
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.SeriesInstanceUID);
a.addValue(u.getAnotherNewUID());
list.put(a);
}
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.StudyInstanceUID);
a.addValue(u.getAnotherNewUID());
list.put(a);
}
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.FrameOfReferenceUID);
a.addValue(u.getAnotherNewUID());
list.put(a);
}
{
Attribute a = new PersonNameAttribute(TagFromName.PatientName);
a.addValue(patientName);
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.PatientID);
a.addValue(patientID);
list.put(a);
}
{
Attribute a = new DateAttribute(TagFromName.PatientBirthDate);
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.PatientSex);
list.put(a);
}
{
Attribute a = new ShortStringAttribute(TagFromName.StudyID);
a.addValue(studyID);
list.put(a);
}
{
Attribute a = new PersonNameAttribute(TagFromName.ReferringPhysicianName);
a.addValue("^^^^");
list.put(a);
}
{
Attribute a = new ShortStringAttribute(TagFromName.AccessionNumber);
list.put(a);
}
{
Attribute a = new IntegerStringAttribute(TagFromName.SeriesNumber);
a.addValue(seriesNumber);
list.put(a);
}
{
Attribute a = new IntegerStringAttribute(TagFromName.InstanceNumber);
a.addValue(instanceNumber);
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.Manufacturer);
a.addValue("PixelMed");
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.DeviceSerialNumber);
a.addValue(new java.rmi.dgc.VMID().toString());
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.SoftwareVersions);
a.addValue(VersionAndConstants.getBuildDate());
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.PatientOrientation);
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.BurnedInAnnotation);
a.addValue("NO");
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.RecognizableVisualFeatures);
a.addValue("NO");
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.ContentQualification);
a.addValue("RESEARCH");
list.put(a);
}
{
Attribute a = new CodeStringAttribute(TagFromName.LossyImageCompression);
a.addValue("00");
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.PositionReferenceIndicator);
list.put(a);
}
{
java.util.Date currentDateTime = new java.util.Date();
String currentDate = new java.text.SimpleDateFormat("yyyyMMdd").format(currentDateTime);
String currentTime = new java.text.SimpleDateFormat("HHmmss.SSS").format(currentDateTime);
{
Attribute a = new DateAttribute(TagFromName.StudyDate);
a.addValue(currentDate);
list.put(a);
}
{
Attribute a = new TimeAttribute(TagFromName.StudyTime);
a.addValue(currentTime);
list.put(a);
}
{
Attribute a = new DateAttribute(TagFromName.SeriesDate);
a.addValue(currentDate);
list.put(a);
}
{
Attribute a = new TimeAttribute(TagFromName.SeriesTime);
a.addValue(currentTime);
list.put(a);
}
{
Attribute a = new DateAttribute(TagFromName.ContentDate);
a.addValue(currentDate);
list.put(a);
}
{
Attribute a = new TimeAttribute(TagFromName.ContentTime);
a.addValue(currentTime);
list.put(a);
}
{
Attribute a = new DateAttribute(TagFromName.InstanceCreationDate);
a.addValue(currentDate);
list.put(a);
}
{
Attribute a = new TimeAttribute(TagFromName.InstanceCreationTime);
a.addValue(currentTime);
list.put(a);
}
{
Attribute a = new ShortStringAttribute(TagFromName.TimezoneOffsetFromUTC);
a.addValue(DateTimeAttribute.getTimeZone(java.util.TimeZone.getDefault(), currentDateTime));
list.put(a);
}
}
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.InstanceCreatorUID);
a.addValue(VersionAndConstants.instanceCreatorUID);
list.put(a);
}
int numberOfFrames =
Attribute.getSingleIntegerValueOrDefault(list, TagFromName.NumberOfFrames, 1);
int samplesPerPixel =
Attribute.getSingleIntegerValueOrDefault(list, TagFromName.SamplesPerPixel, 1);
if (sopClass == null) {
// if modality were not null, could actually attempt to guess SOP Class based on modality here
// :(
sopClass = SOPClass.SecondaryCaptureImageStorage;
if (numberOfFrames > 1) {
if (samplesPerPixel == 1) {
int bitsAllocated =
Attribute.getSingleIntegerValueOrDefault(list, TagFromName.BitsAllocated, 1);
if (bitsAllocated == 8) {
sopClass = SOPClass.MultiframeGrayscaleByteSecondaryCaptureImageStorage;
} else if (bitsAllocated == 16) {
sopClass = SOPClass.MultiframeGrayscaleWordSecondaryCaptureImageStorage;
} else {
Attribute aPixelData = list.getPixelData();
if (aPixelData instanceof OtherFloatAttribute
|| aPixelData instanceof OtherDoubleAttribute) {
sopClass = SOPClass.ParametricMapStorage;
}
}
} else if (samplesPerPixel == 3) {
sopClass = SOPClass.MultiframeTrueColorSecondaryCaptureImageStorage;
}
}
}
if (sopClass.equals(SOPClass.ParametricMapStorage)) {
addParametricMapFrameTypeSharedFunctionalGroup(list);
{
Attribute a = new CodeStringAttribute(TagFromName.ContentLabel);
a.addValue("LABEL1");
list.put(a);
}
{
Attribute a = new LongStringAttribute(TagFromName.ContentDescription);
list.put(a);
}
{
Attribute a = new PersonNameAttribute(TagFromName.ContentCreatorName);
list.put(a);
}
}
if (SOPClass.isEnhancedMultiframeImageStorage(sopClass)) {
if (samplesPerPixel == 1) {
double windowWidth =
Attribute.getSingleDoubleValueOrDefault(list, TagFromName.WindowWidth, 0);
if (windowWidth > 0) {
double windowCenter =
Attribute.getSingleDoubleValueOrDefault(list, TagFromName.WindowCenter, 0);
String voiLUTFunction =
Attribute.getSingleStringValueOrDefault(list, TagFromName.VOILUTFunction, "LINEAR");
FunctionalGroupUtilities.generateVOILUTFunctionalGroup(
list, numberOfFrames, windowWidth, windowCenter, voiLUTFunction);
list.remove(TagFromName.WindowCenter);
list.remove(TagFromName.WindowWidth);
list.remove(TagFromName.VOILUTFunction);
}
}
double rescaleSlope =
Attribute.getSingleDoubleValueOrDefault(list, TagFromName.RescaleSlope, 0);
if (rescaleSlope > 0) {
double rescaleIntercept =
Attribute.getSingleDoubleValueOrDefault(list, TagFromName.RescaleIntercept, 0);
String rescaleType =
Attribute.getSingleStringValueOrDefault(list, TagFromName.RescaleType, "US");
FunctionalGroupUtilities.generatePixelValueTransformationFunctionalGroup(
list, numberOfFrames, rescaleSlope, rescaleIntercept, rescaleType);
list.remove(TagFromName.RescaleSlope);
list.remove(TagFromName.RescaleIntercept);
list.remove(TagFromName.RescaleType);
}
// four values required
{
Attribute a = new CodeStringAttribute(TagFromName.ImageType);
a.addValue("DERIVED");
a.addValue("PRIMARY");
a.addValue("");
a.addValue("");
list.put(a);
}
} else {
// two values will usually do
{
Attribute a = new CodeStringAttribute(TagFromName.ImageType);
a.addValue("DERIVED");
a.addValue("PRIMARY");
list.put(a);
}
}
if (SOPClass.isMultiframeSecondaryCaptureImageStorage(sopClass)) {
if (list.get(TagFromName.PerFrameFunctionalGroupsSequence) != null) {
{
AttributeTagAttribute a = new AttributeTagAttribute(TagFromName.FrameIncrementPointer);
a.addValue(TagFromName.PerFrameFunctionalGroupsSequence);
list.put(a);
}
} else {
if (numberOfFrames > 1) {
{
AttributeTagAttribute a = new AttributeTagAttribute(TagFromName.FrameIncrementPointer);
a.addValue(TagFromName.PageNumberVector);
list.put(a);
}
{
Attribute a = new IntegerStringAttribute(TagFromName.PageNumberVector);
for (int page = 1; page <= numberOfFrames; ++page) {
a.addValue(page);
}
list.put(a);
}
}
}
}
System.err.println(
"CommonConvertedAttributeGeneration.generateCommonAttributes(): SOP Class = " + sopClass);
{
Attribute a = new UniqueIdentifierAttribute(TagFromName.SOPClassUID);
a.addValue(sopClass);
list.put(a);
}
if (SOPClass.isSecondaryCaptureImageStorage(sopClass)) {
{
Attribute a = new CodeStringAttribute(TagFromName.ConversionType);
a.addValue("WSD");
list.put(a);
}
}
if (modality == null) {
// could actually attempt to guess modality based on SOP Class here :(
modality = "OT";
}
{
Attribute a = new CodeStringAttribute(TagFromName.Modality);
a.addValue(modality);
list.put(a);
}
{
Attribute a = new SequenceAttribute(TagFromName.AcquisitionContextSequence);
list.put(a);
}
}
