Examples with ProfileEntity org.karnak.backend.data.entity.ProfileEntity used on opensource projects

Example 1 with ProfileEntity

use of org.karnak.backend.data.entity.ProfileEntity in project karnak by OsiriX-Foundation.

the class Profile method applyAction.

public void applyAction(Attributes dcm, Attributes dcmCopy, HMAC hmac, ProfileItem profilePassedInSequence, ActionItem actionPassedInSequence, AttributeEditorContext context) {
    for (int tag : dcm.tags()) {
        VR vr = dcm.getVR(tag);
        final ExprCondition exprCondition = new ExprCondition(dcmCopy);
        ActionItem currentAction = null;
        ProfileItem currentProfile = null;
        for (ProfileItem profileEntity : profiles.stream().filter(p -> !(p instanceof CleanPixelData)).collect(Collectors.toList())) {
            currentProfile = profileEntity;
            if (profileEntity.getCondition() == null || profileEntity.getCodeName().equals(ProfileItemType.DEFACING.getClassAlias()) || profileEntity.getCodeName().equals(ProfileItemType.CLEAN_PIXEL_DATA.getClassAlias())) {
                currentAction = profileEntity.getAction(dcm, dcmCopy, tag, hmac);
            } else {
                boolean conditionIsOk = (Boolean) ExpressionResult.get(profileEntity.getCondition(), exprCondition, Boolean.class);
                if (conditionIsOk) {
                    currentAction = profileEntity.getAction(dcm, dcmCopy, tag, hmac);
                }
            }
            if (currentAction != null) {
                break;
            }
            if (profileEntity.equals(profilePassedInSequence)) {
                currentAction = actionPassedInSequence;
                break;
            }
        }
        if (!(currentAction instanceof Remove) && !(currentAction instanceof ReplaceNull) && vr == VR.SQ) {
            final ProfileItem finalCurrentProfile = currentProfile;
            final ActionItem finalCurrentAction = currentAction;
            Sequence seq = dcm.getSequence(tag);
            if (seq != null) {
                for (Attributes d : seq) {
                    applyAction(d, dcmCopy, hmac, finalCurrentProfile, finalCurrentAction, context);
                }
            }
        } else {
            if (currentAction != null) {
                try {
                    currentAction.execute(dcm, tag, hmac);
                } catch (final Exception e) {
                    LOGGER.error("Cannot execute the currentAction {} for tag: {}", currentAction, TagUtils.toString(tag), e);
                }
            }
        }
    }
}

Example 2 with ProfileEntity

use of org.karnak.backend.data.entity.ProfileEntity in project karnak by OsiriX-Foundation.

the class Profile method applyCleanPixelData.

public void applyCleanPixelData(Attributes dcmCopy, AttributeEditorContext context, ProfileEntity profileEntity) {
    Object pix = dcmCopy.getValue(Tag.PixelData);
    if ((pix instanceof BulkData || pix instanceof Fragments) && !profileEntity.getMaskEntities().isEmpty() && profiles.stream().anyMatch(p -> p instanceof CleanPixelData)) {
        String sopClassUID = dcmCopy.getString(Tag.SOPClassUID);
        if (!StringUtil.hasText(sopClassUID)) {
            throw new IllegalStateException("DICOM Object does not contain sopClassUID");
        }
        String scuPattern = sopClassUID + ".";
        MaskArea mask = getMask(dcmCopy.getString(Tag.StationName));
        // BurnedInAnnotation
        if (isCleanPixelAllowedDependingImageType(dcmCopy, sopClassUID, scuPattern) && evaluateConditionCleanPixelData(dcmCopy)) {
            context.setMaskArea(mask);
            if (mask == null) {
                throw new IllegalStateException("Clean pixel is not applied: mask not defined in station name");
            }
        } else {
            context.setMaskArea(null);
        }
    }
}

Example 3 with ProfileEntity

use of org.karnak.backend.data.entity.ProfileEntity in project karnak by OsiriX-Foundation.

the class ProfilePipeService method validateProfile.

public ArrayList<ProfileError> validateProfile(ProfilePipeBody profilePipeYml) {
    ProfileEntity newProfileEntity = createNewProfile(profilePipeYml, false);
    ArrayList<ProfileError> profileErrors = new ArrayList<>();
    for (ProfileElementEntity profileElementEntity : newProfileEntity.getProfileElementEntities()) {
        ProfileError profileError = new ProfileError(profileElementEntity);
        profileErrors.add(profileError);
        ProfileItemType t = ProfileItemType.getType(profileElementEntity.getCodename());
        if (t == null) {
            profileError.setError("Cannot find the profile codename: " + profileElementEntity.getCodename());
        } else {
            try {
                t.getProfileClass().getConstructor(ProfileElementEntity.class).newInstance(profileElementEntity);
            } catch (Exception e) {
                profileError.setError(e.getCause().getMessage());
                continue;
            }
        }
    }
    return profileErrors;
}

Example 4 with ProfileEntity

use of org.karnak.backend.data.entity.ProfileEntity in project karnak by OsiriX-Foundation.

the class ProfileLogic method setProfileComponent.

public void setProfileComponent(InputStream stream) {
    try {
        ProfilePipeBody profilePipe = readProfileYaml(stream);
        ArrayList<ProfileError> profileErrors = profilePipeService.validateProfile(profilePipe);
        Predicate<ProfileError> errorPredicate = profileError -> profileError.getError() != null;
        if (profileErrors.stream().noneMatch(errorPredicate)) {
            final ProfileEntity newProfileEntity = profilePipeService.saveProfilePipe(profilePipe, false);
            profileView.getProfileErrorView().removeAll();
            profileView.getProfileGrid().selectRow(newProfileEntity);
            profileView.getProfileComponent().setProfile(newProfileEntity);
            profileView.getProfileElementMainView().setProfile(newProfileEntity);
        } else {
            profileView.getProfileGrid().deselectAll();
            profileView.getProfileErrorView().setView(profileErrors);
            profileView.remove(profileView.getProfileHorizontalLayout());
            profileView.add(profileView.getProfileErrorView());
        }
        if (profilePipe.getDefaultIssuerOfPatientID() != null) {
            openWarningIssuerDialog();
        }
    } catch (YAMLException e) {
        LOGGER.error("Unable to read uploaded YAML", e);
        profileView.getProfileErrorView().setView("Unable to read uploaded YAML file.\n" + "Please make sure it is a YAML file and respects the YAML structure.");
    }
}

Example 5 with ProfileEntity

use of org.karnak.backend.data.entity.ProfileEntity in project karnak by OsiriX-Foundation.

the class ProfileElementRepoTest method shouldFindAllRecords.

/**
 * Test find all.
 */
@Test
void shouldFindAllRecords() {
    // Create an entity to save
    // Profile
    ProfileEntity profileEntity = new ProfileEntity();
    profileEntity.setName("name");
    profileEntity = profileRepo.saveAndFlush(profileEntity);
    // ProfileElement
    ProfileElementEntity entity = new ProfileElementEntity();
    entity.setName("Name");
    entity.setProfileEntity(profileEntity);
    // Save the entity
    LOGGER.info("Saving entity with name [{}]", entity.getName());
    repository.saveAndFlush(entity);
    // Find all
    List<ProfileElementEntity> all = repository.findAll();
    // Test find all
    assertNotNull(all);
    assertTrue(all.size() > 0);
    assertEquals(1, all.size());
    LOGGER.info("Number of entities found [{}]", all.size());
}