Merge pull request #3911 from melissalinkert/dicom-dual-personality

DICOM writer: initial support for dual personality DICOM/TIFF
ome · Jul 31, 2023 · c31c9ef · c31c9ef
2 parents 6c25c68 + 013b211
commit c31c9ef
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Showing 8 changed files with 433 additions and 36 deletions.
diff --git a/components/bio-formats-tools/src/loci/formats/tools/ImageConverter.java b/components/bio-formats-tools/src/loci/formats/tools/ImageConverter.java
@@ -638,12 +638,18 @@ public boolean testConvert(IFormatWriter writer, String[] args)
       ((TiffWriter) writer).setBigTiff(bigtiff);
       ((TiffWriter) writer).setCanDetectBigTiff(!nobigtiff);
     }
+    else if (writer instanceof DicomWriter) {
+      ((DicomWriter) writer).setBigTiff(bigtiff);
+    }
     else if (writer instanceof ImageWriter) {
       IFormatWriter w = ((ImageWriter) writer).getWriter(out);
       if (w instanceof TiffWriter) {
         ((TiffWriter) w).setBigTiff(bigtiff);
         ((TiffWriter) w).setCanDetectBigTiff(!nobigtiff);
       }
+      else if (w instanceof DicomWriter) {
+        ((DicomWriter) w).setBigTiff(bigtiff);
+      }
     }
 
     String format = writer.getFormat();

diff --git a/components/formats-bsd/src/loci/formats/dicom/DicomAttribute.java b/components/formats-bsd/src/loci/formats/dicom/DicomAttribute.java
@@ -670,6 +670,7 @@ public enum DicomAttribute {
     ITEM(0xFFFEE000),
     ITEM_DELIMITATION_ITEM(0xFFFEE00D),
     SEQUENCE_DELIMITATION_ITEM(0xFFFEE0DD),
+    TRAILING_PADDING(0xFFFCFFFC),
 
     // directory structuring elements
     FILE_SET_ID(0x00041130),

diff --git a/components/formats-bsd/src/loci/formats/dicom/DicomTag.java b/components/formats-bsd/src/loci/formats/dicom/DicomTag.java
@@ -134,7 +134,11 @@ else if (vr == IMPLICIT) {
       vr = DicomAttribute.getDefaultVR(tag);
     }
 
-    if (!readValue) {
+    if (!readValue || attribute == PIXEL_DATA) {
+      long skip = elementLength & 0xffffffffL;
+      if (skip > 0 && skip <= in.length() - in.getFilePointer()) {
+        in.skipBytes(skip);
+      }
       return;
     }
 
@@ -352,10 +356,20 @@ private int getNextTag(RandomAccessInputStream in) throws FormatException, IOExc
       return tag;
     }
 
-    if (elementLength < 0 && groupWord == 0x7fe0) {
-      in.skipBytes(12);
-      elementLength = in.readInt();
-      if (elementLength < 0) elementLength = in.readInt();
+    // indicates that we have found pixel data
+    if (groupWord == 0x7fe0) {
+      // the length may legitimately be between 2 and 4 GB
+      long length = elementLength & 0xffffffffL;
+
+      // length of 0xffffffff means undefined length, which is uncommon but allowed
+      if (elementLength == -1 || (length > 0 && length < in.length())) {
+        return tag;
+      }
+      else {
+        in.skipBytes(12);
+        elementLength = in.readInt();
+        if (elementLength < 0) elementLength = in.readInt();
+      }
     }
 
     if (elementLength == 0 && (groupWord == 0x7fe0 || tag == 0x291014)) {

diff --git a/components/formats-bsd/src/loci/formats/in/DicomReader.java b/components/formats-bsd/src/loci/formats/in/DicomReader.java
@@ -672,6 +672,9 @@ else if (child.attribute == OPTICAL_PATH_DESCRIPTION) {
         case EXTENDED_DEPTH_OF_FIELD:
           edf = tag.getStringValue().equalsIgnoreCase("yes");
           break;
+        case TRAILING_PADDING:
+          decodingTags = false;
+          break;
         default:
           in.seek(tag.getEndPointer());
       }
@@ -707,6 +710,9 @@ else if (child.attribute == OPTICAL_PATH_DESCRIPTION) {
       if (m.sizeZ == 0) {
         m.sizeZ = 1;
       }
+      if (m.imageCount == 0) {
+        m.imageCount = 1;
+      }
       if (opticalChannels == 0 || (concatenationNumber == null && ((imagesPerFile / m.sizeZ) % opticalChannels != 0))) {
         opticalChannels = 1;
       }
@@ -1494,8 +1500,8 @@ private void getTile(DicomTile tile, byte[] buf, int x, int y, int w, int h)
         LOGGER.error("attempted to read beyond end of file ({}, {})", tile.fileOffset, tile.file);
         return;
       }
-      stream.seek(tile.fileOffset);
       LOGGER.debug("reading from offset = {}, file = {}", tile.fileOffset, tile.file);
+      stream.seek(tile.fileOffset);
 
       if (tile.isRLE) {
         // plane is compressed using run-length encoding
@@ -1601,7 +1607,14 @@ else if (pt < b.length - 2) {
         options.interleaved = isInterleaved();
         if (tile.isJPEG) codec = new JPEGCodec();
         else codec = new JPEG2000Codec();
-        b = codec.decompress(b, options);
+
+        try {
+          b = codec.decompress(b, options);
+        }
+        catch (NullPointerException e) {
+          LOGGER.debug("Could not read empty or invalid tile", e);
+          return;
+        }
 
         int rowLen = w * bpp;
         int srcRowLen = tile.region.width * bpp;
@@ -1709,7 +1722,10 @@ private void calculatePixelsOffsets(long baseOffset) throws FormatException, IOE
             in.seek(in.getFilePointer() - 1);
           }
         }
-        in.skipBytes(i == 0 ? 64 : 53);
+        if (in.readInt() == 0xe000fffe) {
+          in.skipBytes(12);
+        }
+        in.skipBytes(i == 0 ? 60 : 49);
         while (in.read() == 0);
         offset = in.getFilePointer() - 1;
       }
@@ -1757,7 +1773,7 @@ else if (buf[q] == (byte) 0xff && buf[q + 1] == (byte) 0xd9) {
           }
         }
       }
-      else offset = baseOffset + plane*i;
+      else offset = baseOffset + (long) plane*i;
 
       tilePositions.get(getCoreIndex()).get(i).fileOffset = offset;
       tilePositions.get(getCoreIndex()).get(i).last = i == imagesPerFile - 1;