Several minor bugfixes. Closes #430.

components/bio-formats/src/loci/formats/FileStitcher.java

@@ -924,12 +924,13 @@ protected void initFile(String id) throws FormatException, IOException {
 
     fp = findPattern(currentId);
 
-    reader.setId(fp.getFiles()[0]);
-    if (reader.fileGroupOption(fp.getFiles()[0]) == FormatTools.MUST_GROUP) {
+    if (reader.fileGroupOption(id) == FormatTools.MUST_GROUP) {
       // reader subclass is handling file grouping
       noStitch = true;
+      reader.setId(currentId);
       return;
     }
+    reader.setId(fp.getFiles()[0]);
 
     AxisGuesser guesser = new AxisGuesser(fp, reader.getDimensionOrder(),
       reader.getSizeZ(), reader.getSizeT(), reader.getEffectiveSizeC(),

components/bio-formats/src/loci/formats/in/BioRadReader.java

@@ -143,7 +143,7 @@ public boolean isThisType(RandomAccessInputStream stream) throws IOException {
 
   /* @see loci.formats.IFormatReader#fileGroupOption(String) */
   public int fileGroupOption(String id) throws FormatException, IOException {
-    Location parent = new Location(id).getParentFile();
+    Location parent = new Location(id).getAbsoluteFile().getParentFile();
     String[] list = parent.list();
     for (String f : list) {
       if (checkSuffix(f, "raw") || checkSuffix(f, "xml")) {

components/bio-formats/src/loci/formats/in/InCellReader.java

@@ -426,10 +426,16 @@ protected void initFile(String id) throws FormatException, IOException {
           store.setLogicalChannelName(channelNames.get(q), i, q);
         }
         if (q < emWaves.size()) {
-          store.setLogicalChannelEmWave(emWaves.get(q), i, q);
+          int wave = emWaves.get(q).intValue();
+          if (wave > 0) {
+            store.setLogicalChannelEmWave(emWaves.get(q), i, q);
+          }
         }
         if (q < exWaves.size()) {
-          store.setLogicalChannelExWave(exWaves.get(q), i, q);
+          int wave = exWaves.get(q).intValue();
+          if (wave > 0) {
+            store.setLogicalChannelExWave(exWaves.get(q), i, q);
+          }
         }
       }
     }
@@ -447,12 +453,17 @@ protected void initFile(String id) throws FormatException, IOException {
     for (int i=0; i<seriesCount; i++) {
       int well = getWellFromSeries(i);
       int field = getFieldFromSeries(i);
+      int totalTimepoints =
+        oneTimepointPerSeries ? channelsPerTimepoint.size() : 1;
+      int timepoint = i % totalTimepoints;
+
+      int sampleIndex = field * totalTimepoints + timepoint;
 
       String imageID = MetadataTools.createLSID("Image", i);
-      store.setWellSampleIndex(new Integer(i), 0, well, field);
-      store.setWellSampleImageRef(imageID, 0, well, field);
-      store.setWellSamplePosX(posX.get(field), 0, well, field);
-      store.setWellSamplePosY(posY.get(field), 0, well, field);
+      store.setWellSampleIndex(new Integer(i), 0, well, sampleIndex);
+      store.setWellSampleImageRef(imageID, 0, well, sampleIndex);
+      store.setWellSamplePosX(posX.get(field), 0, well, sampleIndex);
+      store.setWellSamplePosY(posY.get(field), 0, well, sampleIndex);
     }
 
     // populate ROI data

components/bio-formats/src/loci/formats/in/MetamorphReader.java

@@ -741,7 +741,12 @@ protected void initStandardMetadata() throws FormatException, IOException {
       parseUIC1Tags(uic1tagEntry.getValueOffset(),
         uic1tagEntry.getValueCount());
       in.seek(uic4tagEntry.getValueOffset());
+    }
+    catch (IllegalArgumentException exc) { traceDebug(exc); } // unknown tag
+    catch (NullPointerException exc) { traceDebug(exc); }
+    catch (IOException exc) { traceDebug(exc); }
 
+    try {
       // copy ifds into a new array of Hashtables that will accommodate the
       // additional image planes
       IFD firstIFD = ifds.get(0);
@@ -819,7 +824,6 @@ protected void initStandardMetadata() throws FormatException, IOException {
     }
     catch (IllegalArgumentException exc) { traceDebug(exc); } // unknown tag
     catch (NullPointerException exc) { traceDebug(exc); }
-    catch (IOException exc) { traceDebug(exc); }
     catch (FormatException exc) { traceDebug(exc); }
 
     // parse (mangle) TIFF comment
@@ -937,6 +941,7 @@ void parseUIC2Tags(long uic2offset) throws IOException {
 
     for (int i=0; i<mmPlanes; i++) {
       iAsString = intFormatMax(i, mmPlanes);
+      if (in.getFilePointer() + 8 > in.length()) break;
       zDistances[i] = readRational(in).doubleValue();
       addSeriesMeta("zDistance[" + iAsString + "]", zDistances[i]);
 
@@ -971,6 +976,7 @@ void parseUIC2Tags(long uic2offset) throws IOException {
   private void parseUIC4Tags(long uic4offset) throws IOException {
     long saveLoc = in.getFilePointer();
     in.seek(uic4offset);
+    if (in.getFilePointer() + 2 >= in.length()) return;
     short id = in.readShort();
     while (id != 0) {
       switch (id) {

components/bio-formats/src/loci/formats/in/ZeissLSMReader.java

@@ -822,7 +822,7 @@ else if ((block instanceof DetectionChannel) && i > 0) {
     }
     int nLogicalChannels = nextDataChannel == 0 ? 1 : nextDataChannel;
     if (nLogicalChannels == getSizeC()) {
-      splitPlanes = isRGB();
+      if (!splitPlanes) splitPlanes = isRGB();
       core[series].rgb = false;
       if (splitPlanes) core[series].imageCount *= getSizeC();
     }

components/bio-formats/src/loci/formats/in/ZeissZVIReader.java

@@ -963,7 +963,9 @@ private void parseROIs(int imageNum, RandomAccessInputStream s,
       }
 
       s.seek(nameBlock);
-      String roiName = DataTools.stripString(s.readString(s.readInt()));
+      int strlen = s.readInt();
+      if (strlen + s.getFilePointer() > s.length()) continue;
+      String roiName = DataTools.stripString(s.readString(strlen));
 
       s.seek(fontBlock);
       int fontLength = s.readInt();