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));
}
// should be extracted to a utility class ... also used in DoseUtility and
// DoseReporterWithLegacyOCRAndAutoSendToRegistry :(
public static String getQueryRetrieveLevel(AttributeList identifier, Attribute uniqueKey) {
String level = null;
if (identifier != null) {
Attribute a = identifier.get(TagFromName.QueryRetrieveLevel);
if (a != null) {
level = a.getSingleStringValueOrNull();
}
}
if (level == null) {
// QueryRetrieveLevel must have been (erroneously) missing in query response ... see with Dave
// Harvey's code on public server
// so try to guess it from unique key in tree record
// Fixes [bugs.mrmf] (000224) Missing query/retrieve level in C-FIND response causes tree
// select and retrieve to fail
if (uniqueKey != null) {
AttributeTag tag = uniqueKey.getTag();
if (tag != null) {
if (tag.equals(TagFromName.PatientID)) {
level = "PATIENT";
} else if (tag.equals(TagFromName.StudyInstanceUID)) {
level = "STUDY";
} else if (tag.equals(TagFromName.SeriesInstanceUID)) {
level = "SERIES";
} else if (tag.equals(TagFromName.SOPInstanceUID)) {
level = "IMAGE";
}
}
}
log.warning(
"DownloadOrTransmit.getQueryRetrieveLevel(): Guessed missing Query Retrieve Level to be "
+ level);
}
return level;
}
/**
* @param list
* @exception IOException
* @exception DicomException
*/
public CEchoRequestCommandMessage(AttributeList list) throws DicomException, IOException {
groupLength = Attribute.getSingleIntegerValueOrDefault(list, groupLengthTag, 0xffff);
affectedSOPClassUID =
Attribute.getSingleStringValueOrNull(list, TagFromName.AffectedSOPClassUID);
commandField = Attribute.getSingleIntegerValueOrDefault(list, TagFromName.CommandField, 0xffff);
messageID = Attribute.getSingleIntegerValueOrDefault(list, TagFromName.MessageID, 0xffff);
}
/**
* @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));
}
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));
}
protected void setCurrentRemoteQuerySelection(
AttributeList uniqueKeys, Attribute uniqueKey, AttributeList identifier) {
currentRemoteQuerySelectionUniqueKeys = uniqueKeys;
currentRemoteQuerySelectionUniqueKey = uniqueKey;
currentRemoteQuerySelectionRetrieveAE = null;
if (identifier != null) {
Attribute aRetrieveAETitle = identifier.get(TagFromName.RetrieveAETitle);
if (aRetrieveAETitle != null)
currentRemoteQuerySelectionRetrieveAE = aRetrieveAETitle.getSingleStringValueOrNull();
}
if (currentRemoteQuerySelectionRetrieveAE == null) {
// it is legal for RetrieveAETitle to be zero length at all but the lowest levels of
// the query model :( (See PS 3.4 C.4.1.1.3.2)
// (so far the Leonardo is the only one that doesn't send it at all levels)
// we could recurse down to the lower levels and get the union of the value there
// but lets just keep it simple and ...
// default to whoever it was we queried in the first place ...
if (currentRemoteQueryInformationModel != null) {
currentRemoteQuerySelectionRetrieveAE =
currentRemoteQueryInformationModel.getCalledAETitle();
}
}
currentRemoteQuerySelectionLevel = null;
if (identifier != null) {
Attribute a = identifier.get(TagFromName.QueryRetrieveLevel);
if (a != null) {
currentRemoteQuerySelectionLevel = a.getSingleStringValueOrNull();
}
}
if (currentRemoteQuerySelectionLevel == null) {
// QueryRetrieveLevel must have been (erroneously) missing in query response ... see with Dave
// Harvey's code on public server
// so try to guess it from unique key in tree record
// Fixes [bugs.mrmf] (000224) Missing query/retrieve level in C-FIND response causes tree
// select and retrieve to fail
if (uniqueKey != null) {
AttributeTag tag = uniqueKey.getTag();
if (tag != null) {
if (tag.equals(TagFromName.PatientID)) {
currentRemoteQuerySelectionLevel = "PATIENT";
} else if (tag.equals(TagFromName.StudyInstanceUID)) {
currentRemoteQuerySelectionLevel = "STUDY";
} else if (tag.equals(TagFromName.SeriesInstanceUID)) {
currentRemoteQuerySelectionLevel = "SERIES";
} else if (tag.equals(TagFromName.SOPInstanceUID)) {
currentRemoteQuerySelectionLevel = "IMAGE";
}
}
}
log.warning(
"RemotePACs.setCurrentRemoteQuerySelection(): Guessed missing currentRemoteQuerySelectionLevel to be "
+ currentRemoteQuerySelectionLevel);
}
}
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;
}
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 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);
}
}
public void parseDeviceObserver(ContentItem root) throws DicomException {
this.deviceObserverUID = root.getSingleStringValueOrNullOfNamedChild("DCM", "121012");
this.deviceObserverManufacturer = root.getSingleStringValueOrNullOfNamedChild("DCM", "121014");
this.deviceObserverModelName = root.getSingleStringValueOrNullOfNamedChild("DCM", "121015");
this.deviceObserverSerialNumber = root.getSingleStringValueOrNullOfNamedChild("DCM", "121016");
this.deviceObserverPhysicalLocation =
root.getSingleStringValueOrNullOfNamedChild("DCM", "121017");
AttributeList list = root.getAttributeList();
this.manufacturer =
Attribute.getSingleStringValueOrNull(list, new AttributeTag("(0x0008,0x0070)"));
this.institutionName =
Attribute.getSingleStringValueOrNull(list, new AttributeTag("(0x0008,0x0080)"));
this.stationName =
Attribute.getSingleStringValueOrNull(list, new AttributeTag("(0x0008,0x1010)"));
this.institutionalDepartmentName =
Attribute.getSingleStringValueOrNull(list, new AttributeTag("(0x0008,0x1040)"));
this.manufacturersModelName =
Attribute.getSingleStringValueOrNull(list, new AttributeTag("(0x0008,0x1090)"));
this.deviceSerialNumber =
Attribute.getSingleStringValueOrNull(list, new AttributeTag("(0x0018,0x1000)"));
this.softwareVersions =
Attribute.getSingleStringValueOrNull(list, new AttributeTag("(0x0018,0x1020)"));
}
/**
* @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 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));
}
protected CompositeInstanceContext mergePatientContext(
Group group, CompositeInstanceContext newContext) {
if (group.context == null) {
// System.err.println("mergePatientContext(): creating new context for group");
group.context = newContext;
} else {
AttributeList groupList = group.context.getAttributeList();
Iterator<Attribute> newListIterator = newContext.getAttributeList().values().iterator();
while (newListIterator.hasNext()) {
Attribute a = newListIterator.next();
AttributeTag tag = a.getTag();
String groupValue = Attribute.getSingleStringValueOrEmptyString(groupList, tag);
String newValue = a.getSingleStringValueOrEmptyString();
if (!newValue.equals(groupValue)) {
String describeTag = tag + " " + groupList.getDictionary().getFullNameFromTag(tag);
System.err.println(
"mergePatientContext(): in group "
+ group.identity
+ " for "
+ describeTag
+ " values differ between existing group value <"
+ groupValue
+ "> and new value <"
+ newValue
+ ">");
if (newValue.length() > 0
&& (groupValue.length() == 0 || isNonZeroLengthDummyValue(groupValue))) {
System.err.println(
"mergePatientContext(): in group "
+ group.identity
+ " for "
+ describeTag
+ " replacing absent/empty/dummy existing group value with new value <"
+ newValue
+ ">");
groupList.put(a);
}
}
}
}
return group.context;
}
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]);
}
}
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);
}
}
protected void doSomethingWithDicomFileOnMedia(String mediaFileName) {
// logLn("OurFirstPassMediaImporter.doSomethingWithDicomFile(): "+mediaFileName);
try {
DicomInputStream i = new DicomInputStream(new File(mediaFileName));
AttributeList list = new AttributeList();
list.read(i);
i.close();
String sopInstanceUID =
Attribute.getSingleStringValueOrEmptyString(list, TagFromName.SOPInstanceUID);
if (sopInstanceUID.length() > 0) {
String studyInstanceUID =
Attribute.getSingleStringValueOrEmptyString(list, TagFromName.StudyInstanceUID);
if (studyInstanceUID.length() > 0) {
mapOfSOPInstanceUIDToStudyInstanceUID.put(sopInstanceUID, studyInstanceUID);
} else {
throw new DicomException("Missing StudyInstanceUID");
}
{
CompositeInstanceContext cic = new CompositeInstanceContext(list, false /*forSR*/);
// remove all except patient context ...
cic.removeStudy();
cic.removeSeries();
cic.removeEquipment();
cic.removeFrameOfReference();
cic.removeInstance();
cic.removeSRDocumentGeneral();
Group group = addToGroups(list);
// System.err.println("group = "+group);
mergePatientContext(group, cic);
}
} else {
throw new DicomException("Missing SOPInstanceUID");
}
} catch (Exception e) {
logLn("Error: File " + mediaFileName + " exception " + e);
}
}
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 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]);
}
}
/**
* Do something with the referenced DICOM file that has been encountered.
*
* <p>This method needs to be implemented in a sub-class to do anything useful. The default method
* does nothing.
*
* <p>This method does not define any exceptions and hence must handle any errors locally.
*
* @param mediaFileName the fully qualified path name to a DICOM file
*/
protected void doSomethingWithDicomFileOnMedia(String mediaFileName) {
logLn("MediaImporter.doSomethingWithDicomFile(): " + mediaFileName);
try {
AttributeList list = new AttributeList();
list.readOnlyMetaInformationHeader(mediaFileName);
String outputFileName =
Attribute.getSingleStringValueOrEmptyString(list, TagFromName.MediaStorageSOPInstanceUID);
if (outputFileName.length() > 0) {
CopyStream.copy(new File(mediaFileName), new File(outputPath, outputFileName));
} else {
throw new DicomException(
"Cannot extract SOP Instance UID from \""
+ mediaFileName
+ "\" to create output file name - ignoring");
}
} catch (Exception e) {
e.printStackTrace(System.err);
}
}
protected Group addToGroups(AttributeList list) throws DicomException {
Group group = null;
String studyInstanceUID =
Attribute.getSingleStringValueOrEmptyString(list, TagFromName.StudyInstanceUID);
String sopInstanceUID =
Attribute.getSingleStringValueOrEmptyString(list, TagFromName.SOPInstanceUID);
if (sopInstanceUID.length() > 0) {
// System.err.println("addToGroups(): checking "+sopInstanceUID);
group = mapOfSOPInstanceUIDToGroup.get(sopInstanceUID);
// System.err.println("addToGroups(): mapOfSOPInstanceUIDToGroup.get() = "+group);
Set<String> referencedSOPInstanceUIDs = list.findAllNestedReferencedSOPInstanceUIDs();
if (group == null) {
// not already there, so before creating a new group ...
if (studyInstanceUID.length() > 0) {
group = mapOfStudyInstanceUIDToGroup.get(studyInstanceUID);
// System.err.println("addToGroups(): mapOfStudyInstanceUIDToGroup.get() = "+group);
if (group == null) {
// no group with instance in same study, so now try to put it in the same group as any
// referenced instances
if (referencedSOPInstanceUIDs != null) {
for (String referencedSOPInstanceUID : referencedSOPInstanceUIDs) {
group = mapOfSOPInstanceUIDToGroup.get(referencedSOPInstanceUID);
// System.err.println("addToGroups(): mapOfSOPInstanceUIDToGroup.get() = "+group);
if (group != null) {
System.err.println(
"Adding SOP Instance UID "
+ sopInstanceUID
+ " of StudyInstanceUID "
+ studyInstanceUID
+ " based on contained Referenced SOP Instance UID "
+ referencedSOPInstanceUID
+ " to group "
+ group.identity);
break;
}
}
}
} else {
System.err.println(
"Adding SOP Instance UID "
+ sopInstanceUID
+ " based on StudyInstanceUID "
+ studyInstanceUID
+ " to group "
+ group.identity);
}
} else {
throw new DicomException("Missing StudyInstanceUID");
}
if (group
== null) { // i.e., no references or did not find any of the references in existing
// groups
// System.err.println("addToGroups(): creating new group");
group = new Group();
System.err.println(
"Creating new group for SOP Instance UID "
+ sopInstanceUID
+ " based on StudyInstanceUID "
+ studyInstanceUID
+ " group "
+ group.identity);
groups.add(group);
}
}
if (studyInstanceUID.length() > 0) {
Group studyGroup = mapOfStudyInstanceUIDToGroup.get(studyInstanceUID);
if (studyGroup == null) {
System.err.println(
"addToGroups(): mapOfStudyInstanceUIDToGroup.put(studyInstanceUID "
+ studyInstanceUID
+ ")");
mapOfStudyInstanceUIDToGroup.put(studyInstanceUID, group);
} else if (studyGroup != group) {
System.err.println(
"addToGroups(): mapOfStudyInstanceUIDToGroup.get(studyInstanceUID "
+ studyInstanceUID
+ ") != null and != current group");
mergeGroups(group, studyGroup);
}
}
group.add(sopInstanceUID);
Group instanceGroup = mapOfSOPInstanceUIDToGroup.get(sopInstanceUID);
if (instanceGroup == null) {
mapOfSOPInstanceUIDToGroup.put(sopInstanceUID, group);
} else if (instanceGroup != group) {
System.err.println(
"addToGroups(): mapOfSOPInstanceUIDToGroup.get(sopInstanceUID "
+ sopInstanceUID
+ ") != null and != current group");
mergeGroups(group, instanceGroup);
}
if (referencedSOPInstanceUIDs != null) {
// group.addAll(referencedSOPInstanceUIDs);
for (String referencedSOPInstanceUID : referencedSOPInstanceUIDs) {
group.add(referencedSOPInstanceUID);
instanceGroup = mapOfSOPInstanceUIDToGroup.get(referencedSOPInstanceUID);
if (instanceGroup == null) {
mapOfSOPInstanceUIDToGroup.put(referencedSOPInstanceUID, group);
} else if (instanceGroup != group) {
System.err.println(
"addToGroups(): mapOfSOPInstanceUIDToGroup.get(referencedSOPInstanceUID "
+ referencedSOPInstanceUID
+ ") != null and != current group");
mergeGroups(group, instanceGroup);
}
}
}
} else {
throw new DicomException("Missing SOPInstanceUID");
}
return group;
}
/**
* @param list
* @return a single String value, null if cannot be obtained
*/
private static String getDate(AttributeList list) {
return Attribute.getSingleStringValueOrNull(list, TagFromName.StudyDate);
}
/**
* @param list
* @return a single String value, null if cannot be obtained
*/
private static String getLaterality(AttributeList list) {
return Attribute.getSingleStringValueOrNull(list, TagFromName.ImageLaterality);
}
protected void doSomethingWithDicomFileOnMedia(String mediaFileName) {
// logLn("OurFirstPassMediaImporter.doSomethingWithDicomFile(): "+mediaFileName);
try {
DicomInputStream i = new DicomInputStream(new File(mediaFileName));
AttributeList list = new AttributeList();
list.read(i);
i.close();
String sopInstanceUID =
Attribute.getSingleStringValueOrEmptyString(list, TagFromName.SOPInstanceUID);
if (sopInstanceUID.length() > 0) {
Group group = mapOfSOPInstanceUIDToGroup.get(sopInstanceUID);
// System.err.println("group = "+group);
// System.err.println("Groups size = "+groups.size());
if (group == null) {
if (groups.size() == 1) {
group = groups.toArray(singleGroupArray)[0];
} else {
throw new DicomException(
"Cannot merge context for second set if more than one group");
}
}
if (group != null) {
logLn("In group " + group.identity);
if (group.context != null) {
CompositeInstanceContext.removePatient(
list); // remove anything hanging around, such as empty attributes
list.putAll(
group.context
.getAttributeList()); // overwrite all patient context in list that was read
// in
} else {
throw new DicomException(
"Missing group context for SOPInstanceUID on second pass"); // should not be
// possible
}
ClinicalTrialsAttributes.addContributingEquipmentSequence(
list,
true,
new CodedSequenceItem("109103", "DCM", "Modifying Equipment"),
"PixelMed", // Manufacturer
"PixelMed", // Institution Name
"Software Development", // Institutional Department Name
"Bangor, PA", // Institution Address
null, // Station Name
"com.pixelmed.apps.MergeCompositeContext", // Manufacturer's Model Name
null, // Device Serial Number
"Vers. " + VersionAndConstants.getBuildDate(), // Software Version(s)
"Merged patient context");
list.removeGroupLengthAttributes();
list.removeMetaInformationHeaderAttributes();
list.remove(TagFromName.DataSetTrailingPadding);
FileMetaInformation.addFileMetaInformation(
list, TransferSyntax.ExplicitVRLittleEndian, ourAETitle);
File dstFile =
new File(
dstFolderName,
MoveDicomFilesIntoHierarchy.makeHierarchicalPathFromAttributes(list));
if (dstFile.exists()) {
throw new DicomException(
"\""
+ mediaFileName
+ "\": new file \""
+ dstFile
+ "\" already exists - not overwriting");
} else {
File dstParentDirectory = dstFile.getParentFile();
if (!dstParentDirectory.exists()) {
if (!dstParentDirectory.mkdirs()) {
throw new DicomException(
"\""
+ mediaFileName
+ "\": parent directory creation failed for \""
+ dstFile
+ "\"");
}
}
logLn("Writing with new context file " + dstFile);
list.write(dstFile, TransferSyntax.ExplicitVRLittleEndian, true, true);
}
} else {
throw new DicomException(
"Missing group for SOPInstanceUID on second pass"); // should not be possible for
// single set case
}
} else {
throw new DicomException("Missing SOPInstanceUID");
}
} catch (Exception e) {
logLn("Error: File " + mediaFileName + " exception " + e);
}
}
/**
* @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();
}
/** @param list */
private void doCommonConstructorStuff(AttributeList list) throws DicomException {
String sopClassUID = Attribute.getSingleStringValueOrEmptyString(list, TagFromName.SOPClassUID);
if (SOPClass.isImageStorage(sopClassUID)) {
// System.err.println("SuperimposedDicomSegments.doCommonConstructorStuff(): is an image");
SourceImage allFramesImage = new SourceImage(list);
Attribute aSegmentSequence = list.get(TagFromName.SegmentSequence);
Attribute aSharedFunctionalGroupsSequence =
list.get(TagFromName.SharedFunctionalGroupsSequence);
Attribute aPerFrameFunctionalGroupsSequence =
list.get(TagFromName.PerFrameFunctionalGroupsSequence);
int numberOfFrames = allFramesImage.getNumberOfBufferedImages();
if (allFramesImage != null
&& numberOfFrames > 0
&& aSegmentSequence != null
&& aSegmentSequence instanceof SequenceAttribute
&& aSharedFunctionalGroupsSequence != null
&& aSharedFunctionalGroupsSequence instanceof SequenceAttribute
&& aPerFrameFunctionalGroupsSequence != null
&& aPerFrameFunctionalGroupsSequence instanceof SequenceAttribute) {
System.err.println(
"SuperimposedDicomSegments.doCommonConstructorStuff(): have a segmentation object with one or more frames");
SequenceAttribute saSegmentSequence = (SequenceAttribute) aSegmentSequence;
int numberOfSegments = saSegmentSequence.getNumberOfItems();
if (numberOfSegments > 0) {
for (int i = 0; i < numberOfSegments; ++i) {
AttributeList itemList = saSegmentSequence.getItem(i).getAttributeList();
String segmentNumber =
Attribute.getSingleStringValueOrEmptyString(
itemList,
TagFromName
.SegmentNumber); // theoretically supposed to start at 1 and increase by 1,
// but don't trust it
if (segmentNumber.length() > 0) {
int[] recommendedDisplayCIELabValues =
Attribute.getIntegerValues(itemList, TagFromName.RecommendedDisplayCIELabValue);
SegmentInformation si = segmentInformationBySegmentNumber.get(segmentNumber);
if (si == null) {
si = new SegmentInformation(segmentNumber, recommendedDisplayCIELabValues);
segmentInformationBySegmentNumber.put(segmentNumber, si);
} else {
throw new DicomException("Duplicate segment number");
}
} else {
throw new DicomException("Missing segment number");
}
}
} else {
System.err.println(
"SuperimposedDicomSegments.doCommonConstructorStuff(): Error: No segments in segmentation object");
}
SequenceAttribute saSharedFunctionalGroupsSequence =
(SequenceAttribute) aSharedFunctionalGroupsSequence;
SequenceAttribute saPerFrameFunctionalGroupsSequence =
(SequenceAttribute) aPerFrameFunctionalGroupsSequence;
SequenceAttribute sharedSegmentIdentificationSequence =
(SequenceAttribute)
(SequenceAttribute.getNamedAttributeFromWithinSequenceWithSingleItem(
saSharedFunctionalGroupsSequence, TagFromName.SegmentIdentificationSequence));
int nPerFrameFunctionalGroupsSequence =
saPerFrameFunctionalGroupsSequence.getNumberOfItems();
if (nPerFrameFunctionalGroupsSequence == numberOfFrames) {
for (int f = 0; f < numberOfFrames; ++f) {
SequenceAttribute useSegmentIdentificationSequence =
sharedSegmentIdentificationSequence;
if (useSegmentIdentificationSequence == null) {
useSegmentIdentificationSequence =
(SequenceAttribute)
(saPerFrameFunctionalGroupsSequence
.getItem(f)
.getAttributeList()
.get(TagFromName.SegmentIdentificationSequence));
}
if (useSegmentIdentificationSequence != null) {
Attribute aReferencedSegmentNumber =
SequenceAttribute.getNamedAttributeFromWithinSequenceWithSingleItem(
useSegmentIdentificationSequence, TagFromName.ReferencedSegmentNumber);
String referencedSegmentNumber =
aReferencedSegmentNumber == null
? ""
: aReferencedSegmentNumber.getSingleStringValueOrEmptyString();
if (referencedSegmentNumber.length() > 0) {
SortedSet<Integer> framesForSegment =
framesForSegmentBySegmentNumber.get(referencedSegmentNumber);
if (framesForSegment == null) {
framesForSegment = new TreeSet<Integer>();
framesForSegmentBySegmentNumber.put(referencedSegmentNumber, framesForSegment);
}
framesForSegment.add(new Integer(f));
} else {
throw new DicomException("Missing ReferencedSegmentNumber for frame " + f);
}
} else {
throw new DicomException("Missing SegmentIdentificationSequence for frame " + f);
}
}
} else {
throw new DicomException(
"Number of frames "
+ numberOfFrames
+ " does not match number of PerFrameFunctionalGroupsSequence items "
+ nPerFrameFunctionalGroupsSequence);
}
// SortedMap<String,SortedSet<Integer>> framesForSegmentBySegmentNumber
for (String segmentNumber : framesForSegmentBySegmentNumber.keySet()) {
// System.err.println("SuperimposedDicomSegments.doCommonConstructorStuff(): Making
// SourceImageSubset for segmentNumber "+segmentNumber);
SortedSet<Integer> framesForSegment = framesForSegmentBySegmentNumber.get(segmentNumber);
int[] parentFrameNumbers = new int[framesForSegment.size()];
{
int childFrameNumber = 0;
for (Integer parentFrameNumber : framesForSegment) {
// System.err.println("SuperimposedDicomSegments.doCommonConstructorStuff():
// parentFrameNumber["+childFrameNumber+"] = "+parentFrameNumber);
parentFrameNumbers[childFrameNumber++] = parentFrameNumber.intValue();
}
}
SourceImage sourceImageForSegment =
new SourceImageSubset(allFramesImage, parentFrameNumbers);
GeometryOfVolume geometryForSegment =
new GeometryOfVolumeFromAttributeList(list, parentFrameNumbers);
if (!geometryForSegment.isVolumeSampledRegularlyAlongFrameDimension()) {
System.err.println(
"SuperimposedDicomSegments.doCommonConstructorStuff(): Warning: superimposed geometry is not a single regularly sampled volume for segment "
+ segmentNumber);
}
superimposedImagesBySegmentNumber.put(
segmentNumber,
new SuperimposedImage(
sourceImageForSegment,
geometryForSegment,
segmentInformationBySegmentNumber.get(segmentNumber)
.recommendedDisplayCIELabValues));
}
// superimposedGeometry = new GeometryOfVolumeFromAttributeList(list);
// if (!superimposedGeometry.isVolumeSampledRegularlyAlongFrameDimension()) {
// System.err.println("SuperimposedDicomSegments.doCommonConstructorStuff(): Warning:
// superimposed geometry is not a single regularly sampled volume");
// }
} else {
System.err.println(
"SuperimposedDicomSegments.doCommonConstructorStuff(): Error: Not a valid segmentation object");
}
}
}
/**
* 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);
}
}
private static String getFileNameExtensionForCompressedPixelData(AttributeList list) {
String transferSyntaxUID =
Attribute.getSingleStringValueOrEmptyString(list, TagFromName.TransferSyntaxUID);
TransferSyntax ts = new TransferSyntax(transferSyntaxUID);
return ts.getFileNameExtension();
}