/**
* Returns a new descriptor eqiuvalent to this+D. Remember, composition is not commutative for all
* attributes, and may not exist for some. To compose, remember to call
* {@linkDescriptor#isComposable() isComposable} first and try both <code>A.compose (B)</code> and
* <code>B.compose (A)</code>.
*
* @param D The Descriptor to compose with this Descriptor.
* @param scope The attribute scope and mapping.
* @return A new Descriptor that is equivalent to the composition of this and the argument D.
* @throws BadDataException if the compose semantics are not correct.
* @throws UncomposableException this instance of the descriptor cannot be composed. Check
* isComposable!
*/
public Descriptor compose(Descriptor D, EvaluationParameters.ScopeRules scope)
throws BadDataException, UncomposableException {
DescAggregate temp = (DescAggregate) this.clone();
// Unify Descriptions and Spans
temp.span = temp.span.union(D.getFrameSpan());
if (D.getClass().equals(DescSingle.class)) {
if (idList.contains(D.getID()))
throw new BadDataException("Attempting to compose the same descriptor multiple times");
else temp.idList.add(D.getID());
} else {
// First, check to see if there are any dup ID numbers
Iterator iterA = idList.iterator();
Iterator iterB = ((TreeSet) D.getID()).iterator();
Comparable A = (Comparable) iterA.next();
Comparable B = (Comparable) iterB.next();
/// difference will be negative iff A < B, and positive iff A > B.
// I wish java had operator overloading. I really do.
double difference = A.compareTo(B);
while (iterA.hasNext() && iterB.hasNext() && (difference != 0)) {
while ((difference < 0) && (iterA.hasNext() && iterB.hasNext())) {
A = (Comparable) iterA.next();
difference = A.compareTo(B);
}
while ((difference > 0) && (iterA.hasNext() && iterB.hasNext())) {
B = (Comparable) iterB.next();
difference = A.compareTo(B);
}
}
if (difference == 0)
// If there was a dup ID num, return 0
throw new BadDataException("Attempting to compose the same descriptor multiple times");
temp.idList.addAll(((DescAggregate) D).idList);
}
// Unify Attributes
String errMsg = null;
for (Iterator iter = scope.getInScopeAttributesFor(temp); iter.hasNext(); ) {
String currAttrName = (String) iter.next();
int i = temp.getAttributeIndex(currAttrName, scope.getMap());
try {
temp.attributes[i] =
Attribute.compose(
this.span,
this.getAttribute(currAttrName, scope.getMap()),
D.span,
D.getAttribute(currAttrName, scope.getMap()));
} catch (UncomposableException ux) {
if (errMsg == null) {
errMsg = ux.getMessage();
} else {
errMsg += "\n" + ux.getMessage();
}
}
}
if (errMsg != null) System.err.println(errMsg + "\n fix your .epf");
return temp;
}
/**
* 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);
}
}
/**
* @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();
}
}
}