Changeset 4095

Timestamp:

06/04/08 11:09:25 (12 years ago)

Author:

melissa

Message:

• Fixed NPE when calling FluoviewReader.isThisType on a non-TIFF file.
• Fixed index calculation bug when stitching RGB files with more than 4 channels.
• More accurate sizeC calculation for ZVI files.

Location:

trunk/loci/formats

Files:

• FileStitcher.java (modified) (1 diff)
• in/FluoviewReader.java (modified) (1 diff)
• in/ZeissZVIReader.java (modified) (7 diffs)

trunk/loci/formats/FileStitcher.java

@@ -1193 +1193 @@
       posT[0] < readers[sno][fno].getSizeT())
     {
-      if (readers[sno][fno].isRGB()) posC[0] /= lenC[sno][0];
       ino = FormatTools.getIndex(readers[sno][fno], posZ[0], posC[0], posT[0]);
     }

trunk/loci/formats/in/FluoviewReader.java

@@ -446 +446 @@
     String com = TiffTools.getComment(ifd);
     if (com == null) com = "";
+    if (ifd == null) return false;
     return com.indexOf(FLUOVIEW_MAGIC_STRING) != -1 &&
       ifd.containsKey(new Integer(MMHEADER)) ||

trunk/loci/formats/in/ZeissZVIReader.java

@@ -71 +71 @@
   private float pixelSizeX, pixelSizeY, pixelSizeZ;
   private String microscopeName;
-  private Vector emWave, exWave, channelNames;
+  private Vector emWave, exWave;
+  private Hashtable channelNames;
   private Vector whiteValue, blackValue, gammaValue, exposureTime, timestamps;
   private String userName, userCompany, mag, na;
@@ -256 +257 @@
     emWave = new Vector();
     exWave = new Vector();
-    channelNames = new Vector();
+    channelNames = new Hashtable();
     whiteValue = new Vector();
     blackValue = new Vector();
@@ -417 +418 @@
     core.sizeT[0] = tIndices.size();
 
-    int min = Integer.MAX_VALUE;
-    int max = Integer.MIN_VALUE;
-    for (int i=0; i<cIndices.size(); i++) {
-      int v = ((Integer) cIndices.get(i)).intValue();
-      if (v < min) min = v;
-      if (v > max) max = v;
-    }
-
-    int cSize = max - min + 1;
-    if (cSize > cIndices.size()) cSize = cIndices.size() - 1;
-
-    core.sizeC[0] *= cSize;
+    if (channelNames.size() > 0) core.sizeC[0] *= channelNames.size();
+    else core.sizeC[0] *= cIndices.size();
 
     core.imageCount[0] = core.sizeZ[0] * core.sizeT[0] *
@@ -449 +440 @@
 
       while (tileRows * tileColumns > totalTiles) {
-        //if (core.sizeC[0] > 1) core.sizeC[0]--;
         totalTiles =
           offsets.size() / (core.sizeZ[0] * core.sizeC[0] * core.sizeT[0]);
@@ -571 +561 @@
     }
 
-    s = (String[]) channelNames.toArray(new String[0]);
-    channelNames.clear();
-    for (int i=0; i<s.length; i++) {
-      if (!s[i].trim().equals("")) channelNames.add(s[i]);
-    }
+    String[] channelNumbers =
+      (String[]) channelNames.keySet().toArray(new String[0]);
+    Arrays.sort(channelNumbers);
 
     for (int i=0; i<core.sizeC[0]; i++) {
@@ -594 +582 @@
         store.setLogicalChannelExWave(new Integer(ex), 0, idx);
       }
-      if (idx < channelNames.size()) {
-        store.setLogicalChannelName((String) channelNames.get(idx), 0, idx);
+      if (idx < channelNumbers.length) {
+        store.setLogicalChannelName(
+          (String) channelNames.get(channelNumbers[idx]), 0, idx);
       }
 
@@ -936 +925 @@
       else if (key.startsWith("Channel Name")) {
         if (cIndex != -1) {
-          while (cIndex >= channelNames.size()) channelNames.add("");
-          channelNames.setElementAt(value, cIndex);
+          channelNames.put(String.valueOf(cIndex), value);
         }
       }