Add categories for anatomic regions

weasis-dicom-tools/src/main/java/org/dcm4che3/img/stream/ImageDescriptor.java

@@ -18,6 +18,7 @@
 import org.dcm4che3.img.lut.ModalityLutModule;
 import org.dcm4che3.img.lut.VoiLutModule;
 import org.dcm4che3.img.util.DicomUtils;
+import org.weasis.dicom.ref.AnatomicRegion;
 
 /**
  * @author Nicolas Roduit
@@ -33,7 +34,7 @@ public final class ImageDescriptor {
   private final int bitsCompressed;
   private final int pixelRepresentation;
   private final String sopClassUID;
-  private final String bodyPartExamined;
+  private final AnatomicRegion anatomicRegion;
   private final int frames;
   private final List<EmbeddedOverlay> embeddedOverlay;
   private final List<OverlayData> overlayData;
@@ -67,7 +68,7 @@ public ImageDescriptor(Attributes dcm, int bitsCompressed) {
     this.pixelRepresentation = dcm.getInt(Tag.PixelRepresentation, 0);
     this.planarConfiguration = dcm.getInt(Tag.PlanarConfiguration, 0);
     this.sopClassUID = dcm.getString(Tag.SOPClassUID);
-    this.bodyPartExamined = dcm.getString(Tag.BodyPartExamined);
+    this.anatomicRegion = AnatomicRegion.read(dcm);
     this.stationName = dcm.getString(Tag.StationName);
     this.frames = dcm.getInt(Tag.NumberOfFrames, 1);
     this.embeddedOverlay = EmbeddedOverlay.getEmbeddedOverlay(dcm);
@@ -131,8 +132,8 @@ public String getSopClassUID() {
     return sopClassUID;
   }
 
-  public String getBodyPartExamined() {
-    return bodyPartExamined;
+  public AnatomicRegion getAnatomicRegion() {
+    return anatomicRegion;
   }
 
   public String getStationName() {

weasis-dicom-tools/src/main/java/org/weasis/dicom/ref/AnatomicBuilder.java

@@ -10,6 +10,7 @@
 package org.weasis.dicom.ref;
 
 import java.util.Arrays;
+import java.util.EnumMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
@@ -19,6 +20,33 @@
 import org.weasis.core.util.StringUtil;
 
 public class AnatomicBuilder {
+  public enum Category {
+    SURFACE,
+    ALL_RADIO,
+    COMMON,
+    ENDOSCOPY;
+
+    public String getTitle() {
+      return MesCategory.getString(name());
+    }
+
+    @Override
+    public String toString() {
+      return getTitle();
+    }
+  }
+
+  public static final EnumMap<Category, AnatomicItem[]> categoryEnumMap =
+      new EnumMap<>(Category.class);
+
+  static {
+    categoryEnumMap.put(Category.SURFACE, SurfacePart.values());
+    categoryEnumMap.put(Category.ALL_RADIO, BodyPart.values());
+    categoryEnumMap.put(
+        Category.COMMON, getBodyParts(BodyPart::isCommon).toArray(new AnatomicItem[0]));
+    categoryEnumMap.put(
+        Category.ENDOSCOPY, getBodyParts(BodyPart::isEndoscopic).toArray(new AnatomicItem[0]));
+  }
 
   private static final Map<String, BodyPart> CODE_TO_BODY_PART =
       Arrays.stream(BodyPart.values())

weasis-dicom-tools/src/main/java/org/weasis/dicom/ref/AnatomicItem.java

@@ -0,0 +1,22 @@
+/*
+ * Copyright (c) 2024 Weasis Team and other contributors.
+ *
+ * This program and the accompanying materials are made available under the terms of the Eclipse
+ * Public License 2.0 which is available at https://www.eclipse.org/legal/epl-2.0, or the Apache
+ * License, Version 2.0 which is available at https://www.apache.org/licenses/LICENSE-2.0.
+ *
+ * SPDX-License-Identifier: EPL-2.0 OR Apache-2.0
+ */
+package org.weasis.dicom.ref;
+
+public interface AnatomicItem {
+  String getCodeValue();
+
+  String getCodeMeaning();
+
+  CodingScheme getScheme();
+
+  String getLegacyCode();
+
+  boolean isPaired();
+}

weasis-dicom-tools/src/main/java/org/weasis/dicom/ref/AnatomicRegion.java

@@ -0,0 +1,144 @@
+/*
+ * Copyright (c) 2024 Weasis Team and other contributors.
+ *
+ * This program and the accompanying materials are made available under the terms of the Eclipse
+ * Public License 2.0 which is available at https://www.eclipse.org/legal/epl-2.0, or the Apache
+ * License, Version 2.0 which is available at https://www.apache.org/licenses/LICENSE-2.0.
+ *
+ * SPDX-License-Identifier: EPL-2.0 OR Apache-2.0
+ */
+package org.weasis.dicom.ref;
+
+import java.util.HashSet;
+import java.util.Objects;
+import java.util.Set;
+import java.util.stream.Collectors;
+import org.dcm4che3.data.Attributes;
+import org.dcm4che3.data.Sequence;
+import org.dcm4che3.data.Tag;
+import org.dcm4che3.data.VR;
+import org.weasis.core.util.StringUtil;
+import org.weasis.dicom.macro.Code;
+import org.weasis.dicom.ref.AnatomicBuilder.Category;
+
+public class AnatomicRegion {
+
+  private final Category category;
+  private final AnatomicItem region;
+  private final Set<AnatomicModifier> modifiers;
+
+  public AnatomicRegion(AnatomicItem region) {
+    this(null, region, null);
+  }
+
+  public AnatomicRegion(Category category, AnatomicItem region, Set<AnatomicModifier> modifiers) {
+    this.category = category;
+    this.region = Objects.requireNonNull(region);
+    this.modifiers = modifiers == null ? new HashSet<>() : modifiers;
+  }
+
+  public static AnatomicRegion read(Attributes dcm) {
+    if (dcm == null) {
+      return null;
+    }
+    // Get only the first item
+    Attributes regionAttributes = dcm.getNestedDataset(Tag.AnatomicRegionSequence);
+    if (regionAttributes == null) {
+      String bodyPart = dcm.getString(Tag.BodyPartExamined);
+      if (StringUtil.hasText(bodyPart)) {
+        BodyPart item = AnatomicBuilder.getBodyPartFromLegacyCode(bodyPart);
+        if (item != null) {
+          return new AnatomicRegion(item);
+        }
+      }
+      return null;
+    }
+
+    String codeValue = new Code(regionAttributes).getExistingCodeValue();
+    AnatomicItem item = AnatomicBuilder.getBodyPartFromCode(codeValue);
+    if (item == null) {
+      item = AnatomicBuilder.getSurfacePartFromCode(codeValue);
+    }
+
+    AnatomicRegion region = new AnatomicRegion(item);
+    addModifiers(regionAttributes, region);
+    return region;
+  }
+
+  public static void write(Attributes dcm, AnatomicRegion region) {
+    if (dcm == null || region == null) {
+      return;
+    }
+    Attributes regAttributes = new Attributes();
+    AnatomicItem anatomicItem = region.getRegion();
+    regAttributes.setString(Tag.CodeValue, VR.SH, anatomicItem.getCodeValue());
+    regAttributes.setString(Tag.CodeMeaning, VR.LO, anatomicItem.getCodeMeaning());
+    writeScheme(regAttributes, anatomicItem.getScheme());
+    if (anatomicItem.getLegacyCode() != null) {
+      dcm.setString(Tag.BodyPartExamined, VR.CS, anatomicItem.getLegacyCode());
+    }
+
+    Set<AnatomicModifier> modifiers = region.getModifiers();
+    if (modifiers != null && !modifiers.isEmpty()) {
+      Sequence seq =
+          regAttributes.newSequence(Tag.AnatomicRegionModifierSequence, modifiers.size());
+      for (AnatomicModifier modifier : modifiers) {
+        Attributes mod = new Attributes();
+        writeScheme(mod, modifier.getScheme());
+        mod.setString(Tag.CodeValue, VR.SH, modifier.getCodeValue());
+        mod.setString(Tag.CodeMeaning, VR.LO, modifier.getCodeMeaning());
+        seq.add(mod);
+      }
+    }
+    dcm.newSequence(Tag.AnatomicRegionSequence, 1).add(regAttributes);
+  }
+
+  private static void writeScheme(Attributes regionAttributes, CodingScheme scheme) {
+    regionAttributes.setString(Tag.CodingSchemeDesignator, VR.SH, scheme.getDesignator());
+    regionAttributes.setString(Tag.CodingSchemeName, VR.SH, scheme.getCodeName());
+    regionAttributes.setString(Tag.CodingSchemeUID, VR.UI, scheme.getUid());
+  }
+
+  private static void addModifiers(Attributes regionAttributes, AnatomicRegion region) {
+    Sequence seq = regionAttributes.getSequence(Tag.AnatomicRegionModifierSequence);
+    if (seq != null) {
+      for (Attributes attribute : seq) {
+        AnatomicModifier modifier =
+            AnatomicBuilder.getAnatomicModifierFromCode(new Code(attribute).getExistingCodeValue());
+        if (modifier != null) {
+          region.addModifier(modifier);
+        }
+      }
+    }
+  }
+
+  public AnatomicItem getRegion() {
+    return region;
+  }
+
+  public Category getCategory() {
+    return category;
+  }
+
+  public Set<AnatomicModifier> getModifiers() {
+    return modifiers;
+  }
+
+  public void addModifier(AnatomicModifier modifier) {
+    modifiers.add(modifier);
+  }
+
+  public void removeModifier(AnatomicModifier modifier) {
+    modifiers.remove(modifier);
+  }
+
+  @Override
+  public String toString() {
+    String modifiersList =
+        modifiers.stream().map(AnatomicModifier::getCodeMeaning).collect(Collectors.joining(", "));
+    if (StringUtil.hasText(modifiersList)) {
+      modifiersList = " (" + modifiersList + ")";
+    }
+    return region.getCodeMeaning() + modifiersList;
+  }
+}

weasis-dicom-tools/src/main/java/org/weasis/dicom/ref/BodyPart.java

@@ -11,7 +11,7 @@
 
 import static org.weasis.dicom.ref.CodingScheme.SCT;
 
-public enum BodyPart {
+public enum BodyPart implements AnatomicItem {
   ABDOMEN(SCT, 818981001, "ABDOMEN", false, true, false),
   ABDOMEN_AND_PELVIS(SCT, 818982008, "ABDOMENPELVIS", false, true, false),
   ABDOMINAL_AORTA(SCT, 7832008, "ABDOMINALAORTA", false, false, false),

weasis-dicom-tools/src/main/java/org/weasis/dicom/ref/MesCategory.java

@@ -0,0 +1,29 @@
+/*
+ * Copyright (c) 2009-2020 Weasis Team and other contributors.
+ *
+ * This program and the accompanying materials are made available under the terms of the Eclipse
+ * Public License 2.0 which is available at https://www.eclipse.org/legal/epl-2.0, or the Apache
+ * License, Version 2.0 which is available at https://www.apache.org/licenses/LICENSE-2.0.
+ *
+ * SPDX-License-Identifier: EPL-2.0 OR Apache-2.0
+ */
+package org.weasis.dicom.ref;
+
+import java.util.MissingResourceException;
+import java.util.ResourceBundle;
+
+public class MesCategory {
+  private static final String BUNDLE_NAME = "org.weasis.dicom.ref.category"; // NON-NLS
+
+  private static final ResourceBundle RESOURCE_BUNDLE = ResourceBundle.getBundle(BUNDLE_NAME);
+
+  private MesCategory() {}
+
+  public static String getString(String key) {
+    try {
+      return RESOURCE_BUNDLE.getString(key);
+    } catch (MissingResourceException e) {
+      return '!' + key + '!';
+    }
+  }
+}

weasis-dicom-tools/src/main/java/org/weasis/dicom/ref/SurfacePart.java

@@ -13,7 +13,7 @@
 import static org.weasis.dicom.ref.CodingScheme.FMA;
 import static org.weasis.dicom.ref.CodingScheme.SCT;
 
-public enum SurfacePart {
+public enum SurfacePart implements AnatomicItem {
   ANTERIOR_TRIANGLE_OF_NECK(SCT, 182329002, 41, 0, 42),
   CORNEA(SCT, 28726007, 109, 0, 108),
   EYELASH(SCT, 85803001, 105, 0, 104),
@@ -248,6 +248,16 @@ public CodingScheme getScheme() {
     return scheme;
   }
 
+  @Override
+  public String getLegacyCode() {
+    return null;
+  }
+
+  @Override
+  public boolean isPaired() {
+    return left != 0;
+  }
+
   public int getLeft() {
     return left;
   }

weasis-dicom-tools/src/main/resources/org/weasis/dicom/ref/category.properties

@@ -0,0 +1,5 @@
+#Sun May 19 20:36:34 CEST 2024
+SURFACE=Dermatology (surface)
+ALL_RADIO=Radiology
+COMMON=Common
+ENDOSCOPY=Endoscopy

weasis-dicom-tools/src/main/resources/org/weasis/dicom/ref/category_fr.properties

@@ -0,0 +1,5 @@
+#Sun May 19 20:36:34 CEST 2024
+SURFACE=Dermatologie (surface)
+ALL_RADIO=Radiologie
+COMMON=Commun
+ENDOSCOPY=Endoscopie

weasis-dicom-tools/src/test/java/org/dcm4che3/img/TranscoderTest.java

@@ -191,6 +191,8 @@ void dcm2dcmYBR422RawLossy(String lossyUID) throws Exception {
     DicomTranscodeParam params = new DicomTranscodeParam(lossyUID);
     if (lossyUID.equals(UID.JPEGLSNearLossless)) {
       params.getWriteJpegParam().setNearLosslessError(3);
+    } else if (lossyUID.equals(UID.JPEG2000)) {
+      params.getWriteJpegParam().setCompressionRatioFactor(15);
     } else {
       params.getWriteJpegParam().setCompressionQuality(80);
     }

weasis-dicom-tools/src/test/java/org/dcm4che3/img/stream/ImageDescriptorTest.java

@@ -54,7 +54,7 @@ void shouldCreateImageDescriptorWithValidAttributes() {
     assertEquals(15, descriptor.getHighBit());
     assertEquals(1, descriptor.getPixelRepresentation());
     assertEquals("1.2.840.10008.5.1.4.1.1.2", descriptor.getSopClassUID());
-    assertEquals("HEAD", descriptor.getBodyPartExamined());
+    assertEquals("HEAD", descriptor.getAnatomicRegion().getRegion().getLegacyCode());
     assertEquals(1, descriptor.getFrames());
     assertEquals(1, descriptor.getPixelRepresentation());
     assertEquals("COLOR", descriptor.getPixelPresentation());
@@ -96,7 +96,7 @@ void shouldCreateImageDescriptorWithMissingAttributes() {
     assertEquals(7, descriptor.getHighBit());
     assertEquals(0, descriptor.getPixelRepresentation());
     assertNull(descriptor.getSopClassUID());
-    assertNull(descriptor.getBodyPartExamined());
+    assertNull(descriptor.getAnatomicRegion());
     assertEquals(1, descriptor.getFrames());
     assertEquals(0, descriptor.getPixelRepresentation());
     assertNull(descriptor.getModality());

weasis-dicom-tools/src/test/java/org/weasis/dicom/ref/AnatomicBuilderTest.java

@@ -126,10 +126,10 @@ void getSurfacePartFromCode() {
 
     SurfacePart surfacePart = AnatomicBuilder.getSurfacePartFromCode("130319");
     assertNotNull(surfacePart);
-    assertEquals(
-        "Peau de l'hélix postérieur supérieur de l'oreille",
-        surfacePart.toString());
+    assertEquals("Peau de l'hélix postérieur supérieur de l'oreille", surfacePart.toString());
     assertEquals(CodingScheme.DCM, surfacePart.getScheme());
+    assertTrue(surfacePart.isPaired());
+    assertNull(surfacePart.getLegacyCode());
     assertEquals(133, surfacePart.getLeft());
     assertEquals(0, surfacePart.getMiddle());
     assertEquals(132, surfacePart.getRight());