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Apply masks & clean pixel to any type of non compliant image #231

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Apply masks & clean pixel to any type of non compliant image #231

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17 changes: 8 additions & 9 deletions src/main/java/org/karnak/backend/service/profilepipe/Profile.java
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Original file line number Diff line number Diff line change
Expand Up @@ -197,12 +197,11 @@ public void applyCleanPixelData(Attributes dcmCopy, AttributeEditorContext conte
if (!StringUtil.hasText(sopClassUID)) {
throw new IllegalStateException("DICOM Object does not contain sopClassUID");
}
String scuPattern = sopClassUID + ".";
MaskArea mask = getMask(dcmCopy.getString(Tag.StationName));
// A mask must be applied with all the US and Secondary Capture sopClassUID,
// and with
// BurnedInAnnotation
if (isCleanPixelAllowedDependingImageType(dcmCopy, sopClassUID, scuPattern)
if (isCleanPixelAllowedDependingImageType(dcmCopy, sopClassUID)
&& evaluateConditionCleanPixelData(dcmCopy)) {
context.setMaskArea(mask);
if (mask == null) {
Expand All @@ -219,16 +218,16 @@ && evaluateConditionCleanPixelData(dcmCopy)) {
* Determine if the clean pixel should be applied depending on the image type
* @param dcmCopy Attributes
* @param sopClassUID SopClassUID
* @param scuPattern Pattern
* @return true if the clean pixel could be applied
*/
private boolean isCleanPixelAllowedDependingImageType(Attributes dcmCopy, String sopClassUID, String scuPattern) {
boolean isCleanPixelAllowedDependingImageType(Attributes dcmCopy, String sopClassUID) {
// A mask must be applied with all the US and Secondary Capture sopClassUID, and
// with
// BurnedInAnnotation
return scuPattern.startsWith("1.2.840.10008.5.1.4.1.1.6.")
|| scuPattern.startsWith("1.2.840.10008.5.1.4.1.1.7.")
|| scuPattern.startsWith("1.2.840.10008.5.1.4.1.1.3.")
// with BurnedInAnnotation
String sopPattern = sopClassUID + ".";

return sopPattern.startsWith("1.2.840.10008.5.1.4.1.1.6.")
|| sopPattern.startsWith("1.2.840.10008.5.1.4.1.1.7.")
|| sopPattern.startsWith("1.2.840.10008.5.1.4.1.1.3.")
|| sopClassUID.equals("1.2.840.10008.5.1.4.1.1.77.1.1")
|| "YES".equalsIgnoreCase(dcmCopy.getString(Tag.BurnedInAnnotation));
}
Expand Down
87 changes: 81 additions & 6 deletions src/test/java/org/karnak/backend/service/profilepipe/ProfileTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -13,14 +13,10 @@
import org.dcm4che3.data.Tag;
import org.dcm4che3.data.VR;
import org.junit.jupiter.api.Test;
import org.karnak.backend.data.entity.DestinationEntity;
import org.karnak.backend.data.entity.MaskEntity;
import org.karnak.backend.data.entity.ProfileElementEntity;
import org.karnak.backend.data.entity.ProfileEntity;
import org.karnak.backend.data.entity.ProjectEntity;
import org.karnak.backend.data.entity.SecretEntity;
import org.karnak.backend.data.entity.*;
import org.karnak.backend.enums.DestinationType;
import org.karnak.backend.enums.PseudonymType;
import org.springframework.boot.test.context.SpringBootTest;
import org.weasis.dicom.param.AttributeEditorContext;

import java.awt.*;
Expand All @@ -33,6 +29,7 @@
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;

@SpringBootTest
class ProfileTest {

@Test
Expand Down Expand Up @@ -175,4 +172,82 @@ void should_evaluate_condition_clean_pixel_case_include_station_name() {
assertTrue(evaluation);
}

@Test
void cleanPixelData_imageTypeIsXA_forceCleanPixelByStationNumber() {
// Use case : X Ray Angiography that contains identifying information
// but the BurnedInAnnotation attribute is not set
ProfileEntity profileEntity = new ProfileEntity();
Attributes attributes = new Attributes();
attributes.setString(Tag.Modality, VR.CS, "XA");
attributes.setString(Tag.SOPClassUID, VR.UI, "1.2.840.10008.5.1.4.1.1.12.1");
attributes.setString(Tag.StationName, VR.SH, "ICT256");
// Similar object but not from a station that put information in the image
// The BurnedInAnnotation attribute should not be added and the mask not applied
Attributes attributes2 = new Attributes();
attributes2.setString(Tag.Modality, VR.CS, "XA");
attributes2.setString(Tag.SOPClassUID, VR.UI, "1.2.840.10008.5.1.4.1.1.12.1");
attributes2.setString(Tag.StationName, VR.SH, "ICT258");

ProfileElementEntity profileElementEntityAddBurnedAttr = new ProfileElementEntity();
profileElementEntityAddBurnedAttr.setCodename("action.add.tag");
profileElementEntityAddBurnedAttr.setName("Add tag BurnedInAnnotation if does not exist");
profileElementEntityAddBurnedAttr.setCondition("tagValueContains(#Tag.StationName,'ICT256') && !tagIsPresent(#Tag.BurnedInAnnotation)");
profileElementEntityAddBurnedAttr.addArgument(new ArgumentEntity("value", "YES", profileElementEntityAddBurnedAttr));
profileElementEntityAddBurnedAttr.addArgument(new ArgumentEntity("vr", "CS", profileElementEntityAddBurnedAttr));
profileElementEntityAddBurnedAttr.addIncludedTag(new IncludedTagEntity("(0028,0301)", profileElementEntityAddBurnedAttr));
profileElementEntityAddBurnedAttr.setPosition(1);

ProfileElementEntity profileElementEntityCleanPixelPerMachine = new ProfileElementEntity();
profileElementEntityCleanPixelPerMachine.setCodename("expression.on.tags");
profileElementEntityCleanPixelPerMachine.setName("Set BurnedInAnnotation to YES");
profileElementEntityCleanPixelPerMachine.setCondition("tagValueContains(#Tag.StationName,'ICT256')");
profileElementEntityCleanPixelPerMachine.addArgument(new ArgumentEntity("expr", "Replace('YES')", profileElementEntityCleanPixelPerMachine));
profileElementEntityCleanPixelPerMachine.addIncludedTag(new IncludedTagEntity("(0028,0301)", profileElementEntityCleanPixelPerMachine));
profileElementEntityCleanPixelPerMachine.setPosition(2);

Set<ProfileElementEntity> profileElementEntities = new HashSet<>();
ProfileElementEntity profileElementEntityCleanPixelData = new ProfileElementEntity();
profileElementEntityCleanPixelData.setCodename("clean.pixel.data");
profileElementEntityCleanPixelData.setName("nameCleanPixel");
profileElementEntityCleanPixelData.setAction("ReplaceNull");
profileElementEntityCleanPixelData.setPosition(3);

profileElementEntities.add(profileElementEntityCleanPixelData);
profileElementEntities.add(profileElementEntityAddBurnedAttr);
profileElementEntities.add(profileElementEntityCleanPixelPerMachine);
profileEntity.setProfileElementEntities(profileElementEntities);
Profile profile = new Profile(profileEntity);

// First object : should not match the mask application conditions
boolean evaluation = profile.evaluateConditionCleanPixelData(attributes);
String sopClassUID = attributes.getString(Tag.SOPClassUID);
boolean cleanPixelAllowed = profile.isCleanPixelAllowedDependingImageType(attributes, sopClassUID);
// As such the image doesn't comply with the requirements to apply a mask
assertFalse(cleanPixelAllowed && evaluation);

// Second object : should not match the mask application conditions
evaluation = profile.evaluateConditionCleanPixelData(attributes2);
sopClassUID = attributes2.getString(Tag.SOPClassUID);
cleanPixelAllowed = profile.isCleanPixelAllowedDependingImageType(attributes2, sopClassUID);
// As such the image doesn't comply with the requirements to apply a mask
assertFalse(cleanPixelAllowed && evaluation);

// Apply the profile that adds the BurnedInAnnotation attribute to both objects
profile.applyAction(attributes, attributes, null, null, null, null);
profile.applyAction(attributes2, attributes2, null, null, null, null);

// The BurnedInAnnotation attribute is set to YES in the first object
assertEquals("YES", attributes.getString(Tag.BurnedInAnnotation));
// The BurnedInAnnotation attribute does not exist in the second object
assertNull(attributes2.getString(Tag.BurnedInAnnotation));

// First object : should match the mask application conditions
evaluation = profile.evaluateConditionCleanPixelData(attributes);
sopClassUID = attributes.getString(Tag.SOPClassUID);
cleanPixelAllowed = profile.isCleanPixelAllowedDependingImageType(attributes, sopClassUID);
// Since the attribute BurnedInAnnotation is set to YES,
// the application conditions for the mask are fulfilled
assertTrue(cleanPixelAllowed && evaluation);

}
}