Various fixes to allow retrieval of pixel data from truncated TIFFs.

ome · Jan 4, 2011 · 48a5c38 · 48a5c38
1 parent 3e7c104
commit 48a5c38
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Showing 2 changed files with 27 additions and 14 deletions.
diff --git a/components/bio-formats/src/loci/formats/tiff/IFD.java b/components/bio-formats/src/loci/formats/tiff/IFD.java
@@ -709,6 +709,7 @@ public long[] getStripOffsets() throws FormatException {
     if (isTiled() && offsets == null) {
       offsets = getIFDLongArray(STRIP_OFFSETS);
     }
+    if (offsets == null) return null;
 
     for (int i=0; i<offsets.length; i++) {
       if (offsets[i] < 0) {
@@ -750,6 +751,7 @@ public long[] getStripByteCounts() throws FormatException {
       // don't rely on RowsPerStrip, since it's likely that if the file doesn't
       // have the StripByteCounts tag, it also won't have the RowsPerStrip tag
       long[] offsets = getStripOffsets();
+      if (offsets == null) return null;
       int bytesPerSample = getBytesPerSample()[0];
       long imageWidth = getImageWidth();
       long imageLength = getImageLength();
@@ -877,7 +879,10 @@ public void printIFD() {
     for (Integer tag : keySet()) {
       Object value = get(tag);
       String v = null;
-      if ((value instanceof Boolean) || (value instanceof Number) ||
+      if (value == null) {
+        LOGGER.trace("\t{}=null", getIFDTagName(tag.intValue()));
+      }
+      else if ((value instanceof Boolean) || (value instanceof Number) ||
         (value instanceof String) || (value instanceof PhotoInterp) ||
         (value instanceof TiffCompression) || (value instanceof TiffIFDEntry))
       {

diff --git a/components/bio-formats/src/loci/formats/tiff/TiffParser.java b/components/bio-formats/src/loci/formats/tiff/TiffParser.java
@@ -359,6 +359,7 @@ public IFD getIFD(long offset) throws IOException {
         count = (int) ((inputLen - pointer) / bpe);
         LOGGER.trace("getIFDs: truncated {} array elements for tag {}",
           (oldCount - count), tag);
+        if (count < 0) count = oldCount;
       }
       if (count < 0 || count > in.length()) break;
 
@@ -400,6 +401,10 @@ public Object getIFDValue(TiffIFDEntry entry) throws IOException {
     LOGGER.trace("Reading entry {} from {}; type={}, count={}",
       new Object[] {entry.getTag(), offset, type, count});
 
+    if (offset >= in.length()) {
+      return null;
+    }
+
     if (offset != in.getFilePointer()) {
       in.seek(offset);
     }
@@ -661,21 +666,24 @@ public byte[] getSamples(IFD ifd, byte[] buf, int x, int y,
       long[] stripOffsets = ifd.getStripOffsets();
       long[] stripByteCounts = ifd.getStripByteCounts();
 
-      int firstTile = (int) ((y / tileLength) * numTileCols + (x / tileWidth));
-      int lastTile =
-        (int) (((y + height) / tileLength) * numTileCols + (x / tileWidth));
-      lastTile = (int) Math.min(lastTile, stripOffsets.length - 1);
+      if (stripOffsets != null && stripByteCounts != null) {
+        long column = x / tileWidth;
+        int firstTile = (int) ((y / tileLength) * numTileCols + column);
+        int lastTile =
+          (int) (((y + height) / tileLength) * numTileCols + column);
+        lastTile = (int) Math.min(lastTile, stripOffsets.length - 1);
+
+        int offset = 0;
+        for (int tile=firstTile; tile<=lastTile; tile++) {
+          if (stripByteCounts[tile] == numSamples && pixel > 1) {
+            stripByteCounts[tile] *= pixel;
+          }
 
-      int offset = 0;
-      for (int tile=firstTile; tile<=lastTile; tile++) {
-        if (stripByteCounts[tile] == numSamples && pixel > 1) {
-          stripByteCounts[tile] *= pixel;
+          in.seek(stripOffsets[tile]);
+          int len = (int) Math.min(buf.length - offset, stripByteCounts[tile]);
+          in.read(buf, offset, len);
+          offset += len;
         }
-
-        in.seek(stripOffsets[tile]);
-        int len = (int) Math.min(buf.length - offset, stripByteCounts[tile]);
-        in.read(buf, offset, len);
-        offset += len;
       }
       return buf;
     }