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 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));
}
}
/**
* @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));
}
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 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));
}
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));
}
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));
}
/**
* 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);
}
}
/**
* @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();
}
}
}
