MCD: calculate channel count based on metadata, not pixel bytes

In some cases, the number of pixel bytes stored for a particular acquisition
may not match the expected number of bytes, so calculating the channel count
based on the stored number of pixel bytes will cause problems.

Instead of throwing an exception, this sets the channel count to the
number of channels linked to the acquisition, and logs that
some image data may be blank. This more closely matches the behavior
of MCDViewer (the vendor software).

src/main/java/com/glencoesoftware/bioformats2raw/MCDReader.java

@@ -219,35 +219,48 @@ protected void initFile(String id) throws FormatException, IOException {
       m.sizeZ = 1;
       m.sizeT = 1;
 
+      LOGGER.debug("Acquisition size: {} x {}, {} bytes per pixel",
+        acq.sizeX, acq.sizeY, acq.bpp);
+
       int plane = acq.sizeX * acq.sizeY * acq.bpp;
       long totalBytes = acq.end - acq.start;
+      LOGGER.debug("Total pixel bytes: {}", totalBytes);
       if (totalBytes <= 0) {
         LOGGER.debug(
-          "Skipping acquistiion {} with 0 pixel bytes", acq.description);
+          "Skipping acquisition {} with 0 pixel bytes", acq.description);
         acquisitions.remove(acq);
         a--;
         continue;
       }
       long totalPlanes = totalBytes / plane;
+      LOGGER.debug("Detected {} planes in acquisition", totalPlanes);
       if (totalPlanes > Integer.MAX_VALUE) {
         throw new FormatException(
           "Too many channels (" + totalPlanes + ") for series " + core.size());
       }
-      m.sizeC = (int) totalPlanes;
-      m.imageCount = m.sizeC * m.sizeZ * m.sizeT;
-      m.dimensionOrder = "XYCZT";
-      m.littleEndian = true;
-      core.add(m);
 
       // the XML defines a big list of all channels across all acquisitions
       // map each channel to the correct location in the correct acquisition
-      acq.channelIndexes = new int[m.sizeC];
+      acq.channelIndexes = new ArrayList<Integer>();
       for (int c=0; c<channels.size(); c++) {
         Channel channel = channels.get(c);
         if (channel.acqID == acq.id) {
-          acq.channelIndexes[channel.index] = c;
+          while (channel.index >= acq.channelIndexes.size()) {
+            acq.channelIndexes.add(-1);
+          }
+          acq.channelIndexes.set(channel.index, c);
+          m.sizeC++;
         }
       }
+
+      m.imageCount = m.sizeC * m.sizeZ * m.sizeT;
+      if (totalPlanes < m.imageCount) {
+        LOGGER.warn("Not enough pixel bytes in file; images may be blank");
+      }
+
+      m.dimensionOrder = "XYCZT";
+      m.littleEndian = true;
+      core.add(m);
     }
 
     MetadataStore store = makeFilterMetadata();
@@ -263,8 +276,14 @@ protected void initFile(String id) throws FormatException, IOException {
       Acquisition acq = acquisitions.get(a);
       store.setImageName(acq.description, imageIndex);
 
-      for (int c=0; c<acq.channelIndexes.length; c++) {
-        Channel channel = channels.get(acq.channelIndexes[c]);
+      for (int c=0; c<acq.channelIndexes.size(); c++) {
+        int index = acq.channelIndexes.get(c);
+        if (index < 0) {
+          LOGGER.warn("Missing channel definition, channel #{}, image #{}",
+            c, imageIndex);
+          continue;
+        }
+        Channel channel = channels.get(index);
 
         // this is kind of wrong, but the reference viewer
         // exposes both the name and label (which are often slightly different)
@@ -542,7 +561,7 @@ class Acquisition {
     public int bpp;
 
     /** Indexes into list of channels; length matches SizeC. */
-    public int[] channelIndexes;
+    public List<Integer> channelIndexes;
   }
 
   /**