public String toString() {
StringBuffer buffer = new StringBuffer();
buffer.append("Group ");
buffer.append(identity);
buffer.append(" seq ");
buffer.append(sequenceNumber);
buffer.append(":\n");
for (String sopInstanceUID : this) {
buffer.append("\t");
buffer.append(sopInstanceUID);
buffer.append("\n");
}
buffer.append(context.toString());
return buffer.toString();
}
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;
}
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);
}
}
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);
}
}
