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()
/**
* 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);
}
}
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;
}
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!");
}
}
/**
* @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 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;
}
/**
* @param list
* @param document
* @param parent
*/
void addAttributesFromListToNode(AttributeList list, Document document, Node parent) {
DicomDictionary dictionary = list.getDictionary();
Iterator i = list.values().iterator();
while (i.hasNext()) {
Attribute attribute = (Attribute) i.next();
AttributeTag tag = attribute.getTag();
String elementName = dictionary.getNameFromTag(tag);
if (elementName == null) {
elementName = makeElementNameFromHexadecimalGroupElementValues(tag);
}
Node node = document.createElement(elementName);
parent.appendChild(node);
{
Attr attr = document.createAttribute("group");
attr.setValue(HexDump.shortToPaddedHexString(tag.getGroup()));
node.getAttributes().setNamedItem(attr);
}
{
Attr attr = document.createAttribute("element");
attr.setValue(HexDump.shortToPaddedHexString(tag.getElement()));
node.getAttributes().setNamedItem(attr);
}
{
Attr attr = document.createAttribute("vr");
attr.setValue(ValueRepresentation.getAsString(attribute.getVR()));
node.getAttributes().setNamedItem(attr);
}
if (attribute instanceof SequenceAttribute) {
int count = 0;
Iterator si = ((SequenceAttribute) attribute).iterator();
while (si.hasNext()) {
SequenceItem item = (SequenceItem) si.next();
Node itemNode = document.createElement("Item");
Attr numberAttr = document.createAttribute("number");
numberAttr.setValue(Integer.toString(++count));
itemNode.getAttributes().setNamedItem(numberAttr);
node.appendChild(itemNode);
addAttributesFromListToNode(item.getAttributeList(), document, itemNode);
}
} else {
// Attr attr = document.createAttribute("value");
// attr.setValue(attribute.getDelimitedStringValuesOrEmptyString());
// node.getAttributes().setNamedItem(attr);
// node.appendChild(document.createTextNode(attribute.getDelimitedStringValuesOrEmptyString()));
String values[] = null;
try {
values = attribute.getStringValues();
} catch (DicomException e) {
// e.printStackTrace(System.err);
}
if (values != null) {
for (int j = 0; j < values.length; ++j) {
Node valueNode = document.createElement("value");
Attr numberAttr = document.createAttribute("number");
numberAttr.setValue(Integer.toString(j + 1));
valueNode.getAttributes().setNamedItem(numberAttr);
valueNode.appendChild(document.createTextNode(values[j]));
node.appendChild(valueNode);
}
}
}
}
}
/**
* @param list
* @param parent
* @exception NumberFormatException
* @exception DicomException
*/
void addAttributesFromNodeToList(AttributeList list, Node parent)
throws NumberFormatException, DicomException {
if (parent != null) {
Node node = parent.getFirstChild();
while (node != null) {
String elementName = node.getNodeName();
NamedNodeMap attributes = node.getAttributes();
if (attributes != null) {
Node vrNode = attributes.getNamedItem("vr");
Node groupNode = attributes.getNamedItem("group");
Node elementNode = attributes.getNamedItem("element");
if (vrNode != null && groupNode != null && elementNode != null) {
String vrString = vrNode.getNodeValue();
String groupString = groupNode.getNodeValue();
String elementString = elementNode.getNodeValue();
if (vrString != null && groupString != null && elementString != null) {
byte[] vr = vrString.getBytes();
int group = Integer.parseInt(groupString, 16);
int element = Integer.parseInt(elementString, 16);
AttributeTag tag = new AttributeTag(group, element);
if ((group % 2 == 0 && element == 0)
|| (group == 0x0008 && element == 0x0001)
|| (group == 0xfffc && element == 0xfffc)) {
// System.err.println("ignoring group length or length to end or dataset trailing
// padding "+tag);
} else {
if (vrString.equals("SQ")) {
SequenceAttribute a = new SequenceAttribute(tag);
// System.err.println("Created "+a);
if (node.hasChildNodes()) {
Node childNode = node.getFirstChild();
while (childNode != null) {
String childNodeName = childNode.getNodeName();
// System.err.println("childNodeName = "+childNodeName);
if (childNodeName != null && childNodeName.equals("Item")) {
// should check item number, but ignore for now :(
// System.err.println("Adding item to sequence");
AttributeList itemList = new AttributeList();
addAttributesFromNodeToList(itemList, childNode);
a.addItem(itemList);
}
// else may be a #text element in between
childNode = childNode.getNextSibling();
}
}
// System.err.println("Sequence Attribute is "+a);
list.put(tag, a);
} else {
Attribute a = AttributeFactory.newAttribute(tag, vr);
// System.err.println("Created "+a);
if (node.hasChildNodes()) {
Node childNode = node.getFirstChild();
while (childNode != null) {
String childNodeName = childNode.getNodeName();
// System.err.println("childNodeName = "+childNodeName);
if (childNodeName != null && childNodeName.equals("value")) {
// should check value number, but ignore for now :(
String value = childNode.getTextContent();
// System.err.println("Value value = "+value);
if (value != null) {
value =
StringUtilities.removeLeadingOrTrailingWhitespaceOrISOControl(
value); // just in case
a.addValue(value);
}
}
// else may be a #text element in between
childNode = childNode.getNextSibling();
}
}
// System.err.println("Attribute is "+a);
list.put(tag, a);
}
}
}
}
}
node = node.getNextSibling();
}
}
}
/**
* @param filenames
* @exception Exception if internal error
*/
public void loadMultiPanelFromSpecifiedFiles(String filenames[]) throws Exception {
int nFiles = filenames.length;
SingleImagePanel imagePanels[] = new SingleImagePanel[nFiles];
String orientations[][] = new String[nFiles][];
String views[] = new String[nFiles];
String lateralityViewAndModifiers[] = new String[nFiles];
String lateralities[] = new String[nFiles];
int widths[] = new int[nFiles];
int heights[] = new int[nFiles];
PixelSpacing spacing[] = new PixelSpacing[nFiles];
String rowOrientations[] = new String[nFiles];
String columnOrientations[] = new String[nFiles];
HashMap eventContexts = new HashMap();
double maximumHorizontalExtentInMm = 0;
double maximumVerticalExtentInMm = 0;
StructuredReport sr[] = new StructuredReport[nFiles];
int nImages = 0;
int nCAD = 0;
ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
for (int f = 0; f < nFiles; ++f) {
try {
String filename = filenames[f];
DicomInputStream distream = null;
InputStream in = classLoader.getResourceAsStream(filename);
if (in != null) {
distream = new DicomInputStream(in);
} else {
distream = new DicomInputStream(new File(filename));
}
AttributeList list = new AttributeList();
list.read(distream);
if (list.isImage()) {
int i = nImages++;
System.err.println("IMAGE [" + i + "] is file " + f + " (" + filenames[f] + ")");
orientations[i] = getPatientOrientation(list);
// System.err.println("IMAGE ["+i+"] orientation="+(orientations[i] == null &&
// orientations[i].length == 2 ? "" : (orientations[i][0] + " " + orientations[i][1])));
views[i] = getView(list);
// System.err.println("IMAGE ["+i+"] view="+views[i]);
lateralityViewAndModifiers[i] = getImageLateralityViewModifierAndViewModifier(list);
// System.err.println("IMAGE ["+i+"]
// lateralityViewAndModifiers="+lateralityViewAndModifiers[i]);
// System.err.println("File "+filenames[f]+": "+lateralityViewAndModifiers[i]);
lateralities[i] = getLaterality(list);
// System.err.println("IMAGE ["+i+"] laterality="+lateralities[i]);
spacing[i] = new PixelSpacing(list);
// System.err.println("IMAGE ["+i+"] spacing="+spacing[i]);
SourceImage sImg = new SourceImage(list);
BufferedImage img = sImg.getBufferedImage();
widths[i] = sImg.getWidth();
heights[i] = sImg.getHeight();
boolean shareVOIEventsInStudy =
false; // does not seem to work anyway, since adding VOITransform to panel constructor
// :(
EventContext eventContext = new EventContext(Integer.toString(i));
SingleImagePanel imagePanel = makeNewImagePanel(sImg, eventContext);
imagePanel.setDemographicAndTechniqueAnnotations(
new DemographicAndTechniqueAnnotations(list),
"SansSerif",
Font.PLAIN,
10,
Color.pink);
imagePanel.setOrientationAnnotations(
new OrientationAnnotations(rowOrientations[i], columnOrientations[i]),
"SansSerif",
Font.PLAIN,
20,
Color.pink);
imagePanel.setPixelSpacingInSourceImage(
spacing[i].getSpacing(), spacing[i].getDescription());
if (Attribute.getSingleStringValueOrEmptyString(list, TagFromName.VOILUTFunction)
.equals("SIGMOID")) {
imagePanel.setVOIFunctionToLogistic();
}
imagePanels[i] = imagePanel;
} else {
throw new DicomException("Unsupported SOP Class in file " + filenames[f]);
}
} catch (Exception e) { // FileNotFoundException,IOException,DicomException
e.printStackTrace(System.err);
}
}
// int imagesPerRow = nImages; // i.e., 1 -> 1, 2 -> 1, 4 -> 4, 5 -> 4, 8 -> 4
// int imagesPerCol = 1;
int imagesPerRow = nImages >= 8 ? 8 : nImages; // i.e., 1 -> 1, 2 -> 1, 4 -> 4, 5 -> 4, 8 -> 4
int imagesPerCol =
(nImages - 1) / imagesPerRow + 1; // i.e., 1 -> 1, 2 -> 2, 4 -> 1, 5 -> 2, 8 -> 2
int singleWidth = frameWidth / imagesPerRow;
int singleHeight = frameHeight / imagesPerCol;
if (nImages == 1 && singleWidth > singleHeight) {
singleWidth =
singleWidth / 2; // use only half the screen for a single view and a landscape monitor
}
for (int i = 0; i < nImages; ++i) {
DisplayedAreaSelection displayedAreaSelection = null;
displayedAreaSelection =
new DisplayedAreaSelection(
widths[i],
heights[i],
0,
0,
widths[i],
heights[i],
true, // in case spacing was not supplied
0,
0,
0,
0,
0,
false /*crop*/);
imagePanels[i].setDisplayedAreaSelection(displayedAreaSelection);
imagePanels[i].setPreTransformImageRelativeCoordinates(null);
}
SingleImagePanel.deconstructAllSingleImagePanelsInContainer(multiPanel);
multiPanel.removeAll();
multiPanel.setLayout(new GridLayout(imagesPerCol, imagesPerRow));
multiPanel.setBackground(Color.black);
for (int x = 0; x < imagesPerCol; ++x) {
for (int y = 0; y < imagesPerRow; ++y) {
int i = x * imagesPerRow + y;
if (i < nImages) {
imagePanels[i].setPreferredSize(new Dimension(singleWidth, singleHeight));
multiPanel.add(imagePanels[i]);
}
}
}
frame.getContentPane().validate();
frame.getContentPane().repaint();
}
private static Object attrValue(AttributeList attrs) {
return ((Attribute) attrs.get(0)).getValue();
}
private static boolean test(String proto, MBeanServer mbs, ObjectName on) throws Exception {
System.out.println("Testing for protocol " + proto);
JMXConnectorServer cs;
JMXServiceURL url = new JMXServiceURL(proto, null, 0);
try {
cs = JMXConnectorServerFactory.newJMXConnectorServer(url, null, mbs);
} catch (MalformedURLException e) {
System.out.println("System does not recognize URL: " + url + "; ignoring");
return true;
}
cs.start();
JMXServiceURL addr = cs.getAddress();
JMXConnector client = JMXConnectorFactory.connect(addr);
MBeanServerConnection mbsc = client.getMBeanServerConnection();
Object getAttributeExotic = mbsc.getAttribute(on, "Exotic");
AttributeList getAttrs = mbsc.getAttributes(on, new String[] {"Exotic"});
AttributeList setAttrs = new AttributeList();
setAttrs.add(new Attribute("Exotic", new Exotic()));
setAttrs = mbsc.setAttributes(on, setAttrs);
Object invokeExotic = mbsc.invoke(on, "anExotic", new Object[] {}, new String[] {});
MBeanInfo exoticMBI = mbsc.getMBeanInfo(on);
mbsc.setAttribute(on, new Attribute("Exception", Boolean.TRUE));
Exception getAttributeException, setAttributeException, invokeException;
try {
try {
mbsc.getAttribute(on, "Exotic");
throw noException("getAttribute");
} catch (Exception e) {
getAttributeException = e;
}
try {
mbsc.setAttribute(on, new Attribute("Exotic", new Exotic()));
throw noException("setAttribute");
} catch (Exception e) {
setAttributeException = e;
}
try {
mbsc.invoke(on, "anExotic", new Object[] {}, new String[] {});
throw noException("invoke");
} catch (Exception e) {
invokeException = e;
}
} finally {
mbsc.setAttribute(on, new Attribute("Exception", Boolean.FALSE));
}
client.close();
cs.stop();
boolean ok = true;
ok &= checkAttrs("getAttributes", getAttrs);
ok &= checkAttrs("setAttributes", setAttrs);
ok &= checkType("getAttribute", getAttributeExotic, Exotic.class);
ok &= checkType("getAttributes", attrValue(getAttrs), Exotic.class);
ok &= checkType("setAttributes", attrValue(setAttrs), Exotic.class);
ok &= checkType("invoke", invokeExotic, Exotic.class);
ok &= checkType("getMBeanInfo", exoticMBI, ExoticMBeanInfo.class);
ok &= checkExceptionType("getAttribute", getAttributeException, ExoticException.class);
ok &= checkExceptionType("setAttribute", setAttributeException, ExoticException.class);
ok &= checkExceptionType("invoke", invokeException, ExoticException.class);
if (ok) System.out.println("Test passes for protocol " + proto);
return ok;
}