Flex: use plate barcode for grouping, so that truncated files are kept

Without this change, a truncated file would be rejected from the used file list,
which could completely break plate detection.  With an added barcode
check, plates can include truncated files, and files from different
plates will not be inadvertantly grouped together.

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

@@ -251,8 +251,14 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
       new RandomAccessInputStream(getFileHandle(file.file))) {
         IFD ifd;
         if (file.offsets == null) {
-          ifd = file.ifds.get(imageNumber);
-          factor = 1d;
+          if (imageNumber < file.ifds.size()) {
+            ifd = file.ifds.get(imageNumber);
+            factor = 1d;
+          }
+          else {
+            Arrays.fill(buf, (byte) 0);
+            return buf;
+          }
         }
         else {
           // Only the first IFD was read. Hack the IFD to adjust the offset.
@@ -1211,6 +1217,7 @@ private void groupFiles(String[] fileList, MetadataStore store)
     HashMap<String, ArrayList<String>> v = new HashMap<String, ArrayList<String>>();
     Boolean firstCompressed = null;
     int firstIFDCount = 0;
+    String firstBarcode = null;
     for (String file : fileList) {
       LOGGER.warn("parsing {}", file);
       IFD firstIFD = null;
@@ -1226,7 +1233,23 @@ private void groupFiles(String[] fileList, MetadataStore store)
         firstCompressed = compressed;
         firstIFDCount = ifdCount;
       }
-      if (compressed == firstCompressed && ifdCount == firstIFDCount) {
+      String xml = XMLTools.sanitizeXML(firstIFD.getIFDStringValue(FLEX));
+      int barcodeIndex = xml.indexOf("Barcode");
+      String barcode = "";
+      if (barcodeIndex >= 0) {
+        int start = xml.indexOf(">", barcodeIndex) + 1;
+        int end = xml.indexOf("<", barcodeIndex);
+        if (start > 0 && end > 0) {
+          barcode = xml.substring(start, end);
+        }
+      }
+      if (firstBarcode == null) {
+        firstBarcode = barcode;
+      }
+
+      if (compressed == firstCompressed && barcode.equals(firstBarcode) &&
+        ifdCount <= firstIFDCount)
+      {
         int[] well = getWell(file);
         int field = getField(file);
         if (well[0] > nRows) nRows = well[0];