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Frame of reference UID fix #2490

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merged 5 commits into from
Dec 2, 2024
Merged

Frame of reference UID fix #2490

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b023b18
Update AnonymizationServiceImpl.java
michaelkain Nov 7, 2024
86654ea
Merge branch 'develop' into frameOfReferenceUID-fix
LaurentPV Nov 18, 2024
224080c
code review comments
LaurentPV Nov 28, 2024
9e4dafc
Merge branch 'develop' into frameOfReferenceUID-fix
LaurentPV Nov 28, 2024
f94e0e1
log only when studyInstanceUID is reused or generated
LaurentPV Nov 29, 2024
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29 changes: 26 additions & 3 deletions ...ation/src/main/java/org/shanoir/anonymization/anonymization/AnonymizationServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -66,14 +66,15 @@ public void anonymize(ArrayList<File> dicomFiles, String profile) throws Excepti
tagsToDeleteForManufacturer = AnonymizationRulesSingleton.getInstance().getTagsToDeleteForManufacturer();
// init here for multi-threading reasons
Map<String, String> seriesInstanceUIDs = new HashMap<>();
Map<String, String> frameOfReferenceUIDs = new HashMap<>();
Map<String, String> studyInstanceUIDs = new HashMap<>();
Map<String, String> studyIds = new HashMap<>();
LOG.debug("anonymize : totalAmount={}", totalAmount);
int current = 0;
for (int i = 0; i < dicomFiles.size(); ++i) {
final File file = dicomFiles.get(i);
// Perform the anonymization
performAnonymization(file, anonymizationMap, false, "", "", seriesInstanceUIDs, studyInstanceUIDs, studyIds);
performAnonymization(file, anonymizationMap, false, "", "", seriesInstanceUIDs, frameOfReferenceUIDs, studyInstanceUIDs, studyIds);
current++;
final int currentPercent = current * 100 / totalAmount;
LOG.debug("anonymize : anonymization current percent= {} %", currentPercent);
Expand All @@ -99,14 +100,15 @@ public void anonymizeForShanoir(ArrayList<File> dicomFiles, String profile, Stri

// init here for multi-threading reasons
Map<String, String> seriesInstanceUIDs = new HashMap<>();
Map<String, String> frameOfReferenceUIDs = new HashMap<>();
Map<String, String> studyInstanceUIDs = new HashMap<>();
Map<String, String> studyIds = new HashMap<>();
LOG.debug("anonymize : totalAmount={}", totalAmount);
int current = 0;
for (int i = 0; i < dicomFiles.size(); ++i) {
final File file = dicomFiles.get(i);
// Perform the anonymization
performAnonymization(file, anonymizationMap, true, patientName, patientID, seriesInstanceUIDs, studyInstanceUIDs, studyIds);
performAnonymization(file, anonymizationMap, true, patientName, patientID, seriesInstanceUIDs, frameOfReferenceUIDs, studyInstanceUIDs, studyIds);
current++;
final int currentPercent = current * 100 / totalAmount;
LOG.debug("anonymize : anonymization current percent= {} %", currentPercent);
Expand Down Expand Up @@ -156,7 +158,7 @@ private void anonymizePatientMetaData(Attributes attributes, String patientName,
* @throws Exception
*/
public void performAnonymization(final File dicomFile, Map<String, String> anonymizationMap, boolean isShanoirAnonymization,
String patientName, String patientID, Map<String, String> seriesInstanceUIDs,
String patientName, String patientID, Map<String, String> seriesInstanceUIDs, Map<String, String> frameOfReferenceUIDs,
Map<String, String> studyInstanceUIDs, Map<String, String> studyIds) throws Exception {
DicomInputStream din = null;
DicomOutputStream dos = null;
Expand Down Expand Up @@ -217,6 +219,8 @@ public void performAnonymization(final File dicomFile, Map<String, String> anony
anonymizeSOPInstanceUID(tagInt, datasetAttributes, mediaStorageSOPInstanceUIDGenerated);
} else if (tagInt == Tag.SeriesInstanceUID) {
anonymizeSeriesInstanceUID(tagInt, datasetAttributes, seriesInstanceUIDs);
} else if (tagInt == Tag.FrameOfReferenceUID) {
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anonymizeFrameOfReferenceUID(tagInt, datasetAttributes, frameOfReferenceUIDs);
} else if (tagInt == Tag.StudyInstanceUID) {
anonymizeStudyInstanceUID(tagInt, datasetAttributes, studyInstanceUIDs);
} else if (tagInt == Tag.StudyID) {
Expand Down Expand Up @@ -350,6 +354,25 @@ private void anonymizeSOPInstanceUID(int tagInt, Attributes attributes, String m
anonymizeTagAccordingToVR(attributes, tagInt, mediaStorageSOPInstanceUID);
}

private void anonymizeFrameOfReferenceUID(int tagInt, Attributes attributes, Map<String, String> frameOfReferenceUIDs) {
String value;
if (frameOfReferenceUIDs != null && frameOfReferenceUIDs.size() != 0
&& frameOfReferenceUIDs.get(attributes.getString(tagInt)) != null) {
value = frameOfReferenceUIDs.get(attributes.getString(tagInt));
} else {
UIDGeneration generator = new UIDGeneration();
String newUID = null;
try {
newUID = generator.getNewUID();
} catch (Exception e) {
LOG.error(e.getMessage());
}
value = newUID;
frameOfReferenceUIDs.put(attributes.getString(tagInt), value);
}
anonymizeTagAccordingToVR(attributes, tagInt, value);
}

private void anonymizeSeriesInstanceUID(int tagInt, Attributes attributes, Map<String, String> seriesInstanceUIDs) {
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String value;
if (seriesInstanceUIDs != null && seriesInstanceUIDs.size() != 0
Expand Down
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