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));
}
}
public void TestSafePrivateGEMRRelated_AddedToList() throws Exception {
{
String value = "MySequence";
Attribute a = new LongStringAttribute(new AttributeTag(0x0019, 0x109E));
a.addValue(value);
testIsNotRemovedAndRetainsValue(
"Internal Pulse Sequence Name",
new AttributeTag(0x0019, 0x0010),
"GEMS_ACQU_01",
a,
value);
}
{
String value = "35";
Attribute a = new SignedLongAttribute(new AttributeTag(0x0025, 0x1007));
a.addValue(value);
testIsNotRemovedAndRetainsValue(
"Images In Series", new AttributeTag(0x0025, 0x0010), "GEMS_SERS_01", a, value);
}
{
String expectValue = "0\\0\\0\\2";
Attribute a = new DecimalStringAttribute(new AttributeTag(0x0043, 0x106F));
a.addValue("0");
a.addValue("0");
a.addValue("0");
a.addValue("2");
testIsNotRemovedAndRetainsValue(
"Scanner Table Entry + Gradient Coil Selected",
new AttributeTag(0x0043, 0x0010),
"GEMS_PARM_01",
a,
expectValue);
}
}
/**
* @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 static AttributeList addParametricMapFrameTypeSharedFunctionalGroup(AttributeList list)
throws DicomException {
Attribute aFrameType = new CodeStringAttribute(TagFromName.FrameType);
aFrameType.addValue("DERIVED");
aFrameType.addValue("PRIMARY");
aFrameType.addValue(
""); // do not have a value for Image Flavor, but value is required to be present
aFrameType.addValue(
""); // do not have a value for Derived Pixel Contrast, but value is required to be present
list =
FunctionalGroupUtilities.generateFrameTypeSharedFunctionalGroup(
list, TagFromName.ParametricMapFrameTypeSequence, aFrameType);
return 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 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 TestDecimalStringAttributeLocaleEffect_Float_DefaultLocale() throws Exception {
float value1 = 39.76f;
float value2 = -56356.457457f;
float value3 = 0f;
float value4 = 7.45345345e-21f;
{
Attribute a = new DecimalStringAttribute(TagFromName.ContourData);
a.addValue(value1);
a.addValue(value2);
a.addValue(value3);
a.addValue(value4);
float[] returnedValues = a.getFloatValues();
assertEquals("Default", value1, returnedValues[0]);
assertEquals("Default", value2, returnedValues[1]);
assertEquals("Default", value3, returnedValues[2]);
assertEquals("Default", value4, returnedValues[3]);
}
}
public void TestDecimalStringAttributeLocaleEffect_Double_DefaultLocale() throws Exception {
double value1 = 39.76d;
double value2 = -56356.457457d;
double value3 = 0d;
double value4 = 7.45345345e-21d;
{
Attribute a = new DecimalStringAttribute(TagFromName.ContourData);
a.addValue(value1);
a.addValue(value2);
a.addValue(value3);
a.addValue(value4);
double[] returnedValues = a.getDoubleValues();
assertEquals("Default", value1, returnedValues[0]);
assertEquals("Default", value2, returnedValues[1]);
assertEquals("Default", value3, returnedValues[2]);
assertEquals("Default", value4, returnedValues[3]);
}
}
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));
}
public void TestDecimalStringAttributeLocaleEffect_Double_AllAvailableLocales() throws Exception {
double value1 = 39.76d;
double value2 = -56356.457457d;
double value3 = 0d;
double value4 = 7.45345345e-21d;
Locale[] localesToTest = Locale.getAvailableLocales();
for (Locale l : localesToTest) {
// System.err.println("Testing effect on DS getDoubleValues() of default locale "+l);
Locale.setDefault(l);
Attribute a = new DecimalStringAttribute(TagFromName.ContourData);
a.addValue(value1);
a.addValue(value2);
a.addValue(value3);
a.addValue(value4);
double[] returnedValues = a.getDoubleValues();
assertEquals(l.toString(), value1, returnedValues[0]);
assertEquals(l.toString(), value2, returnedValues[1]);
assertEquals(l.toString(), value3, returnedValues[2]);
assertEquals(l.toString(), value4, returnedValues[3]);
}
}
protected void performRetrieve(
AttributeList uniqueKeys, String selectionLevel, String retrieveAE) {
try {
AttributeList identifier = new AttributeList();
if (uniqueKeys != null) {
identifier.putAll(uniqueKeys);
{
AttributeTag t = TagFromName.QueryRetrieveLevel;
Attribute a = new CodeStringAttribute(t);
a.addValue(selectionLevel);
identifier.put(t, a);
}
currentRemoteQueryInformationModel.performHierarchicalMoveFrom(identifier, retrieveAE);
} else {
// else do nothing, since no unique key to specify what to retrieve
log.warning("UniqueKeys for retrieval are null");
}
} catch (Exception e) {
e.printStackTrace(System.err);
}
}
/**
* 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);
}
}