Merge pull request #4168 from melissalinkert/gh-4165

DICOM reader: better handling of nested sequences that include pixel data

Author: dgault

components/formats-bsd/src/loci/formats/dicom/DicomTag.java

@@ -310,15 +310,33 @@ else if (elementLength <= 44) {
                 break;
               }
               else if (child.attribute == PIXEL_DATA) {
-                stop = fp;
-                break;
+                child.parent = this;
+                children.add(child);
+                if (child.elementLength == -1) {
+                  // look for end of sequence
+                  long seek = fp - 2;
+                  int nextTag = 0;
+                  while (seek < in.length() && (nextTag != SEQUENCE_DELIMITATION_ITEM.getTag() && nextTag != ITEM_DELIMITATION_ITEM.getTag())) {
+                    seek += 2;
+                    in.seek(seek);
+                    try {
+                      nextTag = getNextTag(in);
+                    }
+                    catch (Exception e) {
+                    }
+                    if (nextTag == 0xfeffdde0 || nextTag == 0xfeff0d0e) {
+                      in.order(!in.isLittleEndian());
+                      break;
+                    }
+                  }
+                }
               }
               else if (child.attribute != ITEM && child.attribute != ITEM_DELIMITATION_ITEM) {
                 child.parent = this;
                 children.add(child);
               }
             }
-            if (elementLength == 0) {
+            if (elementLength <= 0) {
               elementLength = (int) (stop - start);
             }
             in.seek(stop);
@@ -438,6 +456,7 @@ private int getLength(RandomAccessInputStream in) throws IOException {
 
     switch (vr) {
       case OB:
+      case OV:
       case OW:
       case SQ:
       case UN:
@@ -700,6 +719,17 @@ else if (!(value instanceof long[])) {
     }
   }
 
+  /**
+   * See https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_7.8.html
+   *
+   * @return true if this is a private content creator tag
+   */
+  public boolean isPrivateContentCreator() {
+    int highWord = (tag >> 16) & 0xffff;
+    int lowWord = tag & 0xffff;
+    return highWord % 2 == 1 && lowWord == 0x0010;
+  }
+
   @Override
   public String toString() {
     if (key == null) {

components/formats-bsd/src/loci/formats/in/DicomReader.java

@@ -37,9 +37,11 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import com.google.common.collect.ImmutableMap;
 import com.google.common.collect.ImmutableMap.Builder;
@@ -127,6 +129,8 @@ public class DicomReader extends SubResolutionFormatReader {
 
   private List<DicomTag> tags;
 
+  private Set<Integer> privateContentHighWords = new HashSet<Integer>();
+
   // -- Constructor --
 
   /** Constructs a new DICOM reader. */
@@ -368,6 +372,7 @@ public void close(boolean fileOnly) throws IOException {
       concatenationNumber = null;
       edf = false;
       tags = null;
+      privateContentHighWords.clear();
     }
   }
 
@@ -1168,6 +1173,10 @@ else if (infoString.startsWith("MONOCHROME")) {
    * rely upon the original metadata table.
    */
   private void addOriginalMetadata(String key, DicomTag info) {
+    if (info.isPrivateContentCreator()) {
+      privateContentHighWords.add(info.tag >> 16);
+    }
+
     if (info.value != null && !(info.value instanceof byte[]) &&
       !(info.value instanceof short[]))
     {
@@ -1179,7 +1188,8 @@ private void addOriginalMetadata(String key, DicomTag info) {
       }
     }
     if (info.attribute != PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE &&
-      info.attribute != REFERENCED_IMAGE_NAVIGATION_SEQUENCE)
+      info.attribute != REFERENCED_IMAGE_NAVIGATION_SEQUENCE &&
+      !privateContentHighWords.contains(info.tag >> 16))
     {
       for (DicomTag child : info.children) {
         String childKey = DicomAttribute.formatTag(child.tag);