Better indexed color logic; still broken in various cases though.

ome · Jun 2, 2010 · 9d31f0f · 9d31f0f
1 parent f7df373
commit 9d31f0f
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Showing 2 changed files with 31 additions and 11 deletions.
diff --git a/components/loci-plugins/src/loci/plugins/in/ImagePlusReader.java b/components/loci-plugins/src/loci/plugins/in/ImagePlusReader.java
@@ -306,11 +306,20 @@ private List<ImagePlus> concatenate(List<ImagePlus> imps) {
   private List<ImagePlus> applyColors(List<ImagePlus> imps) {
     final ImporterOptions options = process.getOptions();
 
-    // CTR FIXME - problems with single channel data
-    // CTR FIXME - problems with sizeC > 7
     // CTR FIXME - problems with default color mode
     int mode = -1;
-    if (options.isColorModeComposite()) mode = CompositeImage.COMPOSITE;
+    int sizeC = process.getReader().getSizeC();
+    if (sizeC == 1) {
+      // NB: Cannot use CompositeImage for single-channel images.
+      // CTR FIXME finish sizeC==1 case
+      loci.plugins.BF.warn(options.isQuiet(), "sizeC = 1");//TEMP
+    }
+    else if (sizeC > 7) {
+      // NB: Cannot use CompositeImage when there are more than seven channels.
+      // CTR FIXME finish sizeC>7 case
+      loci.plugins.BF.warn(options.isQuiet(), "sizeC > 7");//TEMP
+    }
+    else if (options.isColorModeComposite()) mode = CompositeImage.COMPOSITE;
     else if (options.isColorModeColorized()) mode = CompositeImage.COLOR;
     else if (options.isColorModeGrayscale()) mode = CompositeImage.GRAYSCALE;
     else if (options.isColorModeCustom()) mode = CompositeImage.COLOR;

diff --git a/components/loci-plugins/src/loci/plugins/in/ImportProcess.java b/components/loci-plugins/src/loci/plugins/in/ImportProcess.java
@@ -415,24 +415,35 @@ private void initializeStack() throws FormatException, IOException {
     }
     r.setId(options.getId());
 
-    boolean fillIndexed;
+    final boolean fillIndexed;
     if (r.isIndexed()) {
+      final int bpp = FormatTools.getBytesPerPixel(r.getPixelType());
+      final byte[][] lut8 = r.get8BitLookupTable();
+      final boolean defaultColorMode = options.isColorModeDefault();
+
+      // NB: ImageJ only supports 8-bit RGB color tables.
+      // In addition, we only keep the indices in default color mode.
+      final boolean keepColorTable = defaultColorMode &&
+        bpp == 1 && lut8 != null && lut8.length >= 1 && lut8.length <= 3;
+
       if (r.isFalseColor()) {
-        // false color; never fill indices
+        // false color; never fill the indices
         fillIndexed = false;
+        if (!keepColorTable) {
+          // warn the user that we'll have to throw away the color table
+          BF.warn(options.isQuiet(),
+            "false color table will be lost: " + getIdName());
+        }
       }
       else {
-        // true color; fill indices unless 8-bit RGB with default color mode
-        int bpp = FormatTools.getBytesPerPixel(r.getPixelType());
-        byte[][] lut8 = r.get8BitLookupTable();
-        boolean defaultColorMode = options.isColorModeDefault();
-        fillIndexed = !defaultColorMode || bpp > 1 || lut8 == null || lut8[0].length > 3;
+        // true color; if we can't keep the color table, then fill the indices
+        fillIndexed = !keepColorTable;
       }
     }
     else fillIndexed = false; // no need to fill non-indexed data
     if (fillIndexed) {
       r = channelFiller = new ChannelFiller(r);
-      BF.warn(options.isQuiet(), "Index values will be lost");
+      BF.warn(options.isQuiet(), "index values will be lost: " + getIdName());
     }
 
     r = channelSeparator = new ChannelSeparator(r);