Prevent File Channel Null Pointer Exceptions when writing large data sets

java/pom.xml

@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.micro-manager.ndtiffstorage</groupId>
     <artifactId>NDTiffStorage</artifactId>
-    <version>2.19.2</version>
+    <version>2.19.3</version>
     <packaging>jar</packaging>
     <name>NDTiff Storage file format</name>
     <description>Java-based writer and reader used for NDTiffStorage format and NDRAM storage</description>

java/src/main/java/org/micromanager/ndtiffstorage/NDTiffWriter.java

@@ -292,9 +292,48 @@ private long unsignInt(int i) {
    public void overwritePixels(String indexKey, Object pixels, boolean rgb) throws IOException {
       long pixelOffset = indexMap_.get(indexKey).pixOffset_;
       Buffer pixBuff = getPixelBuffer(pixels, rgb);
+      if (fileChannel_ == null) {
+         // This writer has already been finishedWriting() (its file was rotated/closed as
+         // the file set grew). Pixels still need to be overwritten in place -- e.g. when
+         // building low-res pyramid levels, a downsampled tile receives contributions from
+         // several full-res tiles, and the tile's first write may live in an earlier,
+         // now-closed file. Reopen the file read-write just for this in-place write, then
+         // close it again so we don't leak file descriptors for every rotated file.
+         overwritePixelsReopening(pixBuff, pixelOffset);
+         return;
+      }
       fileChannelWrite(pixBuff, pixelOffset);
    }
 
+   /**
+    * Overwrite pixels in place in a file whose channel has been closed (after
+    * finishedWriting()). Opens the existing file read-write at {@code position}, writes the
+    * buffer, and closes -- the writer stays in its finished state. The index entry's
+    * pixOffset_ is an absolute file offset, so no header re-parsing is needed.
+    */
+   private void overwritePixelsReopening(final Buffer buffer, final long position)
+           throws IOException {
+      buffer.rewind();
+      ByteBuffer byteBuffer = (ByteBuffer) buffer;
+      RandomAccessFile raf = null;
+      try {
+         raf = new RandomAccessFile(filename_, "rw");
+         FileChannel ch = raf.getChannel();
+         // A single positional write is not guaranteed to write the whole buffer; loop
+         // until it is fully written, advancing the file position by the bytes written.
+         long pos = position;
+         while (byteBuffer.hasRemaining()) {
+            pos += ch.write(byteBuffer, pos);
+         }
+      } finally {
+         // Recycle in finally so a write/IO failure cannot leak a large direct buffer.
+         masterMPTiffStorage_.tryRecycleLargeBuffer(byteBuffer);
+         if (raf != null) {
+            raf.close();
+         }
+      }
+   }
+
    private IndexEntryData writeIFD(String indexKey, Object pixels, byte[] metadata,
                                    boolean rgb, int imageHeight, int imageWidth, int bitDepth
                             ) throws IOException {