From c21ddb683a38cda157726745d4ab7558abeb8df0 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Thu, 15 Mar 2007 15:41:30 +0000
Subject: [PATCH] Only allow merging if there are 2 or 3 channels; otherwise
 display a warning (and the grayscale stack).

---
 loci/plugins/Importer.java | 31 +++++++++++++------------------
 1 file changed, 13 insertions(+), 18 deletions(-)

diff --git a/loci/plugins/Importer.java b/loci/plugins/Importer.java
index 6bb2c89c9d8..719ed1f1e1c 100644
--- a/loci/plugins/Importer.java
+++ b/loci/plugins/Importer.java
@@ -1138,7 +1138,7 @@ private void displayStack(ImagePlus imp, IFormatReader r,
     try {
       // convert to RGB if needed
 
-      if (mergeChannels && r.getSizeC(id) > 1) {
+      if (mergeChannels && r.getSizeC(id) > 1 && r.getSizeC(id) < 4) {
         int c = r.getSizeC(id);
         ImageStack s = imp.getStack();
         ImageStack newStack = new ImageStack(s.getWidth(), s.getHeight());
@@ -1155,31 +1155,26 @@ private void displayStack(ImagePlus imp, IFormatReader r,
         int sizeZ = r.getSizeZ(id);
         int sizeT = r.getSizeT(id);
 
-        int extraC = 1;
-        if (c > 4) {
-          extraC *= (c % 3 == 0 ? 4 : 3);
-          c /= extraC;
-        }
-
         for (int z=0; z<sizeZ; z++) {
           for (int t=0; t<sizeT; t++) {
             byte[][] bytes = new byte[c][];
-            for (int ch1=0; ch1<extraC; ch1++) {
-              for (int ch2=0; ch2<c; ch2++) {
-                int ndx = r.getIndex(id, z, ch1*c + ch2, t) + 1;
-                bytes[ch2] = (byte[]) s.getProcessor(ndx).getPixels();
-              }
-              ColorProcessor cp =
-                new ColorProcessor(s.getWidth(), s.getHeight());
-              cp.setRGB(bytes[0], bytes[1], bytes.length == 3 ? bytes[2] :
-                new byte[s.getWidth() * s.getHeight()]);
-              int ndx = r.getIndex(id, z, ch1*c + c - 1, t) + 1;
-              newStack.addSlice(s.getSliceLabel(ndx), cp);
+            for (int ch1=0; ch1<c; ch1++) {
+              int ndx = r.getIndex(id, z, ch1, t) + 1;
+              bytes[ch1] = (byte[]) s.getProcessor(ndx).getPixels();
             }
+            ColorProcessor cp =
+              new ColorProcessor(s.getWidth(), s.getHeight());
+            cp.setRGB(bytes[0], bytes[1], bytes.length == 3 ? bytes[2] :
+              new byte[s.getWidth() * s.getHeight()]);
+            int ndx = r.getIndex(id, z, c - 1, t) + 1;
+            newStack.addSlice(s.getSliceLabel(ndx), cp);
           }
         }
         imp.setStack(imp.getTitle(), newStack);
       }
+      else if (mergeChannels && r.getSizeC(id) >= 4) {
+        IJ.showMessage("Can only merge 2 or 3 channels.");
+      }
 
       imp.setDimensions(
         imp.getStackSize() / (imp.getNSlices() * imp.getNFrames()),