Altered the original work-around logic so that when a .ets file has n…

…o associated metadata block in the .vsi file, its contents are omitted from the series list, and the file is treated the same way as the blob_*.meta files, which is to say, their names are included in the 'extraFiles' list, and they are otherwise ignored.

components/formats-gpl/src/loci/formats/in/CellSensReader.java

@@ -772,14 +772,28 @@ else if (zCount > 0) {
         setCoreIndex(index);
         String ff = files.get(s);
         /**
-         * If there are fewer metadata 'pyramids' defined in the vsi than there
-         * are frame_*.ets files, we are missing the metadata associated with
-         * one or more frame_*.ets files.  In this case we need to dynamically
-         * match the metadata we do have with the appropriate frame_*.ets file.
+         * If there are more frame_*.ets files than there are metadata 'pyramids'
+         * defined in the .vsi, then we have orphaned frame files.  In this case
+         * we need to determine which are the valid frame files and which are 
+         * the orphans.  The valid ones need to be matched with the appropriate
+         * metadata blocks in the vsi, and the orphaned ones need to be ignored.
         */
-        boolean missingMetadata = pyramids.size() < (files.size() - 1);
+        boolean hasOrphanEtsFiles = pyramids.size() < (files.size() - 1);
         try (RandomAccessInputStream stream = new RandomAccessInputStream(ff)) {
-            parseETSFile(stream, ff, s, missingMetadata);
+            boolean validFrameFile = parseETSFile(stream, ff, s, hasOrphanEtsFiles);
+            /*
+             * If this frame file is an orphan, "undo" the work that was done for
+             * it and change its status to being an "extra" file.
+             */
+             if (!validFrameFile) {
+                core.remove(core.size()-1);
+                extraFiles.add(files.get(s));
+                files.remove(s);
+                usedFiles = files.toArray(new String[files.size()]);
+                s--;
+                seriesCount--;
+                continue;
+             }
         }
 
         ms.littleEndian = compressionType.get(index) == RAW;
@@ -1191,8 +1205,8 @@ else if (dim.equals("T")) {
     return buf;
   }
 
-  private void parseETSFile(RandomAccessInputStream etsFile, String file, int s,
-                            boolean missingMetadata)
+  private boolean parseETSFile(RandomAccessInputStream etsFile, String file, int s,
+                            boolean hasOrphanEtsFiles)
     throws FormatException, IOException
   {
     fileMap.put(core.size() - 1, file);
@@ -1293,12 +1307,13 @@ private void parseETSFile(RandomAccessInputStream etsFile, String file, int s,
     HashMap<String, Integer> dimOrder = new HashMap<String, Integer>();
     Pyramid pyramid = null;
     /**
-    * If there is metadata missing from the vsi file, we need to see if we can match up
-    * this frame_*.ets file with its correct metadata block if it exists.  To do that we
-    * search the metadata blocks (ie 'pyramids') for the one whose width and height are
-    * within the correct range for this frame_*.ets file.
-    */
-    if (missingMetadata) {
+    * If there are orphaned .ets files with this vsi file, we need to determine whether
+    * the current one is an orphan or a legit file.  The logic to determine this is to
+    * see of there is a metadata block (ie 'pyramid') whose width and height are
+    * within the correct range for this .ets file.  If there is no matching metadata
+    * block, then we have to assume this is an orphan
+    **/
+    if (hasOrphanEtsFiles) {
       int maxXAtRes0 = 0;
       int maxYAtRes0 = 0;
       for (TileCoordinate t : tmpTiles) {
@@ -1316,14 +1331,24 @@ private void parseETSFile(RandomAccessInputStream etsFile, String file, int s,
             break;
         }
       }
+      /**
+      * No matching metadata block.  This is an orphan ets file.  Undo and erase 
+      * all the data elements that have been gathered up for this .ets file.
+      **/
+      if (pyramid == null) {
+        nDimensions.remove(nDimensions.size() - 1);
+        compressionType.remove(compressionType.size() - 1);
+        tileX.remove(tileX.size() - 1);
+        tileY.remove(tileY.size() - 1);
+        backgroundColor.remove(getCoreIndex());
+        tileOffsets.remove(tileOffsets.size()-1);
+        return(false);
+      }
     }
     else {
       pyramid = pyramids.get(s);
     }
-
-    if (pyramid != null) {
-      dimOrder = pyramid.dimensionOrdering;
-    }
+    dimOrder = pyramid.dimensionOrdering;
 
     for (TileCoordinate t : tmpTiles) {
       int resolution = usePyramid ? t.coordinate[t.coordinate.length - 1] : 0;
@@ -1418,24 +1443,9 @@ private void parseETSFile(RandomAccessInputStream etsFile, String file, int s,
         maxC[resolution] = t.coordinate[cIndex];
       }
     }
-    /**
-     * If this ets file has an associated metadata block, grab the correct width and height,
-     * and link it to the full metadata block.
-     */
-    if (pyramid != null) {
-      ms.sizeX = pyramid.width;
-      ms.sizeY = pyramid.height;
-      ms.seriesMetadata = pyramid.originalMetadata;
-    }
-    else {
-    /**
-     * Otherwise, compute the closest approximation, since the real info couldn't be found.
-     */
-      ms.sizeX = (maxX[0] + 1) * tileX.get(tileX.size()-1);
-      ms.sizeY = (maxY[0] + 1) * tileY.get(tileY.size()-1);
-      ms.seriesMetadata = new Hashtable<String, Object>();
-      ms.seriesMetadata.put("Metadata", "Not Found"); // leave a trail that the metadata was missing for this ets.
-    }
+    ms.sizeX = pyramid.width;
+    ms.sizeY = pyramid.height;
+    ms.seriesMetadata = pyramid.originalMetadata;
     ms.sizeZ = maxZ[0] + 1;
     if (maxC[0] > 0) {
       ms.sizeC *= (maxC[0] + 1);
@@ -1529,6 +1539,7 @@ else if (newResolution.sizeY > maxSizeY) {
 
       ms.resolutionCount = finalResolution;
     }
+    return(true);
   }
 
   private int convertPixelType(int pixelType) throws FormatException {