Changeset 6324

Timestamp:

05/17/10 00:40:34 (10 years ago)

Author:

curtis

Message:

Add API for assigning custom colors programmatically.

Location:

trunk/components/loci-plugins/src/loci/plugins

Files:

• colorize/Colorizer.java (modified) (1 diff)
• in/ColorDialog.java (moved) (moved from trunk/components/loci-plugins/src/loci/plugins/colorize/CustomColorChooser.java) (5 diffs)
• in/ImagePlusReader.java (modified) (5 diffs)
• in/ImportProcess.java (modified) (3 diffs)
• in/ImportStep.java (modified) (1 diff)
• in/ImporterOptions.java (modified) (3 diffs)
• in/ImporterPrompter.java (modified) (2 diffs)

trunk/components/loci-plugins/src/loci/plugins/colorize/Colorizer.java

@@ -326 +326 @@
 
   private static byte[][] promptForColor(int channel, int series) {
+    /*
     CustomColorChooser chooser = new CustomColorChooser(
       "Color Chooser - Channel " + channel, null, series, channel);
 
     Color color = chooser.getColor();
+    */
+    Color color = null; // CTR TEMP
     if (color == null) return null;
     double redIncrement = ((double) color.getRed()) / 255;

trunk/components/loci-plugins/src/loci/plugins/in/ColorDialog.java

@@ -1 +1 @@
 //
-// CustomColorChooser.java
+// ColorDialog.java
 //
 
@@ -24 +24 @@
 */
 
-package loci.plugins.colorize;
+package loci.plugins.in;
 
 import ij.gui.GenericDialog;
@@ -37 +37 @@
 import java.awt.event.TextEvent;
 import java.awt.event.TextListener;
+import java.util.ArrayList;
 import java.util.List;
 
+import loci.plugins.util.ImageProcessorReader;
 import loci.plugins.util.WindowTools;
 
 /**
- * Adapted from {@link ij.gui.ColorChooser}.
+ * Bio-Formats Importer custom color chooser dialog box.
+ *
+ * Heavily adapted from {@link ij.gui.ColorChooser}.
  * ColorChooser is not used because there is no way to change the slider
  * labels—this means that we can't record macros in which custom colors
@@ -48 +52 @@
  *
  * <dl><dt><b>Source code:</b></dt>
- * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/CustomColorChooser.java">Trac</a>,
- * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/CustomColorChooser.java">SVN</a></dd></dl>
+ * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/loci-plugins/src/loci/plugins/ColorDialog.java">Trac</a>,
+ * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/components/loci-plugins/src/loci/plugins/ColorDialog.java">SVN</a></dd></dl>
  *
  * @author Melissa Linkert linkert at wisc.edu
+ * @author Curtis Rueden ctrueden at wisc.edu
  */
-public class CustomColorChooser implements TextListener {
-  List<TextField> colors;
-  Panel panel;
-  Color initialColor;
-  int red, green, blue;
-  String title;
+public class ColorDialog extends ImporterDialog {
 
-  private int series, channel;
+  // -- Constants --
 
-  public CustomColorChooser(String title, Color initialColor, int series,
-    int channel)
-  {
-      this.title = title;
-      if (initialColor == null) initialColor = Color.BLACK;
-      this.initialColor = initialColor;
-      red = initialColor.getRed();
-      green = initialColor.getGreen();
-      blue = initialColor.getBlue();
-      this.series = series;
-      this.channel = channel;
+  /** Default custom colors for each channel. */
+  private static final Color[] DEFAULT_COLORS = {
+    Color.red,
+    Color.green,
+    Color.blue,
+    Color.white,
+    Color.cyan,
+    Color.magenta,
+    Color.yellow
+  };
+  private static final Dimension SWATCH_SIZE = new Dimension(100, 50);
+
+  // -- Fields --
+
+  private List<TextField> colors;
+
+  // -- Constructor --
+
+  public ColorDialog(ImportProcess process) {
+    super(process);
   }
 
-  // -- ColorChooser API methods --
+  // -- ImporterDialog methods --
 
-  /**
-   * Displays a color selection dialog and returns the color
-   *  selected by the user.
-   */
-  public Color getColor() {
-    GenericDialog gd = new GenericDialog(title);
-    gd.addSlider(makeLabel("Red:"), 0, 255, red);
-    gd.addSlider(makeLabel("Green:"), 0, 255, green);
-    gd.addSlider(makeLabel("Blue:"), 0, 255, blue);
-
-    panel = new Panel();
-    Dimension prefSize = new Dimension(100, 50);
-    panel.setPreferredSize(prefSize);
-    panel.setMinimumSize(prefSize);
-    panel.setBackground(initialColor);
-    gd.addPanel(panel, GridBagConstraints.CENTER, new Insets(10, 0, 0, 0));
-
-    colors = WindowTools.getNumericFields(gd);
-    for (int i=0; i<colors.size(); i++) {
-      colors.get(i).addTextListener(this);
-    }
-    gd.showDialog();
-    if (gd.wasCanceled()) return null;
-    int red = (int) gd.getNextNumber();
-    int green = (int) gd.getNextNumber();
-    int blue = (int) gd.getNextNumber();
-    return new Color(red, green, blue);
+  @Override
+  protected boolean needPrompt() {
+    return !process.isWindowless() && options.isColorModeCustom();
   }
 
-  public void textValueChanged(TextEvent e) {
-    int red = getColorValue(0);
-    int green = getColorValue(1);
-    int blue = getColorValue(2);
-    panel.setBackground(new Color(red, green, blue));
-    panel.repaint();
+  @Override
+  protected GenericDialog constructDialog() {
+    GenericDialog gd = new GenericDialog("Bio-Formats Custom Colorization");
+
+    // CTR TODO - avoid problem with MAX_SLIDERS in GenericDialog
+    final ImageProcessorReader reader = process.getReader();
+    final List<Panel> swatches = new ArrayList<Panel>();
+    for (int s=0; s<process.getSeriesCount(); s++) {
+      if (!options.isSeriesOn(s)) continue;
+      reader.setSeries(s);
+      for (int c=0; c<reader.getSizeC(); c++) {
+        Color color = options.getCustomColor(s, c);
+        if (color == null) color = DEFAULT_COLORS[c % DEFAULT_COLORS.length];
+        gd.addSlider(makeLabel("Red:", s, c), 0, 255, color.getRed());
+        gd.addSlider(makeLabel("Green:", s, c), 0, 255, color.getGreen());
+        gd.addSlider(makeLabel("Blue:", s, c), 0, 255, color.getBlue());
+
+        Panel swatch = createSwatch(color);
+        gd.addPanel(swatch, GridBagConstraints.CENTER, new Insets(5, 0, 5, 0));
+        swatches.add(swatch);
+      }
+    }
+
+    // change swatch colors when sliders move
+    List<TextField> colorFields = gd.getNumericFields();
+    attachListeners(colorFields, swatches);
+
+    WindowTools.addScrollBars(gd);
+
+    return gd;
+  }
+
+  @Override
+  protected boolean harvestResults(GenericDialog gd) {
+    final ImageProcessorReader reader = process.getReader();
+    for (int s=0; s<process.getSeriesCount(); s++) {
+      if (!options.isSeriesOn(s)) continue;
+      reader.setSeries(s);
+      for (int c=0; c<reader.getSizeC(); c++) {
+        int red = (int) gd.getNextNumber();
+        int green = (int) gd.getNextNumber();
+        int blue = (int) gd.getNextNumber();
+        Color color = new Color(red, green, blue);
+        options.setCustomColor(s, c, color);
+      }
+    }
+    return true;
   }
 
   // -- Helper methods --
 
-  private int getColorValue(int index) {
-    int color = (int) Tools.parseDouble(colors.get(index).getText());
+  private String makeLabel(String baseLabel, int s, int c) {
+    return "Series_" + s + "_Channel_" + c + "_" + baseLabel;
+  }
+
+  private Panel createSwatch(Color color) {
+    Panel swatch = new Panel();
+    swatch.setPreferredSize(SWATCH_SIZE);
+    swatch.setMinimumSize(SWATCH_SIZE);
+    swatch.setMaximumSize(SWATCH_SIZE);
+    swatch.setBackground(color);
+    return swatch;
+  }
+
+  private void attachListeners(List<TextField> colors, List<Panel> swatches) {
+    int colorIndex = 0, swatchIndex = 0;
+    while (colorIndex < colors.size()) {
+      final TextField redField = colors.get(colorIndex++);
+      final TextField greenField = colors.get(colorIndex++);
+      final TextField blueField = colors.get(colorIndex++);
+      final Panel swatch = swatches.get(swatchIndex++);
+      TextListener textListener = new TextListener() {
+        public void textValueChanged(TextEvent e) {
+          int red = getColorValue(redField);
+          int green = getColorValue(greenField);
+          int blue = getColorValue(blueField);
+          swatch.setBackground(new Color(red, green, blue));
+          swatch.repaint();
+        }
+      };
+      redField.addTextListener(textListener);
+      greenField.addTextListener(textListener);
+      blueField.addTextListener(textListener);
+    }
+  }
+
+  private int getColorValue(TextField colorField) {
+    int color = 0;
+    try {
+      color = Integer.parseInt(colorField.getText());
+    }
+    catch (NumberFormatException exc) { }
     if (color < 0) color = 0;
     if (color > 255) color = 255;
@@ -123 +188 @@
   }
 
-  private String makeLabel(String baseLabel) {
-    return "Series_" + series + "_Channel_" + channel + "_" + baseLabel;
-  }
-
 }

trunk/components/loci-plugins/src/loci/plugins/in/ImagePlusReader.java

@@ -131 +131 @@
 
     // beginning timing
-    long startTime = System.currentTimeMillis();
-    long time = startTime;
+    startTiming();
 
     ImageProcessorReader reader = process.getReader();
@@ -147 +146 @@
     for (int s=0; s<reader.getSeriesCount(); s++) {
       if (!options.isSeriesOn(s)) continue;
-      reader.setSeries(s);
-
-      boolean[] load = new boolean[reader.getImageCount()];
-      int cBegin = process.getCBegin(s);
-      int cEnd = process.getCEnd(s);
-      int cStep = process.getCStep(s);
-      int zBegin = process.getZBegin(s);
-      int zEnd = process.getZEnd(s);
-      int zStep = process.getZStep(s);
-      int tBegin = process.getTBegin(s);
-      int tEnd = process.getTEnd(s);
-      int tStep = process.getTStep(s);
-      for (int c=cBegin; c<=cEnd; c+=cStep) {
-        for (int z=zBegin; z<=zEnd; z+=zStep) {
-          for (int t=tBegin; t<=tEnd; t+=tStep) {
-            //int index = r.isOrderCertain() ? r.getIndex(z, c, t) : c;
-            int index = reader.getIndex(z, c, t);
-            load[index] = true;
-          }
-        }
-      }
-      int total = 0;
-      for (int j=0; j<reader.getImageCount(); j++) if (load[j]) total++;
-
-      FileInfo fi = new FileInfo();
-
-      // populate other common FileInfo fields
-      String idDir = process.getIdLocation() == null ?
-        null : process.getIdLocation().getParent();
-      if (idDir != null && !idDir.endsWith(File.separator)) {
-        idDir += File.separator;
-      }
-      fi.fileName = process.getIdName();
-      fi.directory = idDir;
-
-      ImageStack stackB = null; // for byte images (8-bit)
-      ImageStack stackS = null; // for short images (16-bit)
-      ImageStack stackF = null; // for floating point images (32-bit)
-      ImageStack stackO = null; // for all other images (24-bit RGB)
-
-      Region region = process.getCropRegion(s);
-      int sizeX = reader.getSizeX(), sizeY = reader.getSizeY();
-      if (options.doCrop()) {
-        // bounds checking for cropped region
-        if (region.x < 0) region.x = 0;
-        if (region.y < 0) region.y = 0;
-        if (region.width <= 0 || region.x + region.width > sizeX) {
-          region.width = sizeX - region.x;
-        }
-        if (region.height <= 0 || region.y + region.height > sizeY) {
-          region.height = sizeX - region.y;
-        }
-      }
-      else {
-        // obtain entire image plane
-        region.x = region.y = 0;
-        region.width = sizeX;
-        region.height = sizeY;
-      }
-
-      int q = 0;
-
-      // dump OME-XML to ImageJ's description field, if available
-      try {
-        ServiceFactory factory = new ServiceFactory();
-        OMEXMLService service = factory.getInstance(OMEXMLService.class);
-        fi.description = service.getOMEXML(process.getOMEMetadata());
-      }
-      catch (DependencyException de) { }
-      catch (ServiceException se) { }
-
-      if (options.isVirtual()) {
-        boolean doMerge = false; //options.isMergeChannels();
-        boolean doColorize = false; //options.isColorize();
-
-        reader.setSeries(s);
-        // NB: ImageJ 1.39+ is required for VirtualStack
-        BFVirtualStack virtualStackB = new BFVirtualStack(options.getId(),
-          reader, doColorize, doMerge, options.isRecord());
-        stackB = virtualStackB;
-        if (doMerge) {
-          for (int j=0; j<reader.getImageCount(); j++) {
-            int[] zct = reader.getZCTCoords(j);
-            if (zct[1] > 0) continue;
-            ChannelMerger channelMerger = new ChannelMerger(reader);
-            int index = channelMerger.getIndex(zct[0], zct[1], zct[2]);
-            String label = constructSliceLabel(index,
-              channelMerger, process.getOMEMetadata(), s,
-              process.getZCount(s), process.getCCount(s), process.getTCount(s));
-            virtualStackB.addSlice(label);
-          }
-        }
-        else {
-          for (int j=0; j<reader.getImageCount(); j++) {
-            String label = constructSliceLabel(j,
-              reader, process.getOMEMetadata(), s,
-              process.getZCount(s), process.getCCount(s), process.getTCount(s));
-            virtualStackB.addSlice(label);
-          }
-        }
-      }
-      else {
-        // CTR CHECK
-        //if (r.isIndexed()) colorModels = new IndexColorModel[r.getSizeC()];
-
-        for (int i=0; i<reader.getImageCount(); i++) {
-          if (!load[i]) continue;
-
-          // limit message update rate
-          long clock = System.currentTimeMillis();
-          if (clock - time >= 100) {
-            String sLabel = reader.getSeriesCount() > 1 ?
-              ("series " + (s + 1) + ", ") : "";
-            String pLabel = "plane " + (i + 1) + "/" + total;
-            notifyListeners(new StatusEvent("Reading " + sLabel + pLabel));
-            time = clock;
-          }
-          notifyListeners(new StatusEvent(q++, total, null));
-
-          String label = constructSliceLabel(i,
-            reader, process.getOMEMetadata(), s,
-            process.getZCount(s), process.getCCount(s), process.getTCount(s));
-
-          // get image processor for ith plane
-          ImageProcessor[] p;
-          p = reader.openProcessors(i, region.x, region.y,
-            region.width, region.height);
-          ImageProcessor ip = p[0];
-          if (p.length > 1) {
-            ip = ImagePlusTools.makeRGB(p).getProcessor();
-          }
-          if (ip == null) {
-            throw new FormatException("Cannot read ImageProcessor #" + i);
-          }
-
-          // CTR CHECK
-          //int channel = r.getZCTCoords(i)[1];
-          //if (colorModels != null && p.length == 1) {
-          //  colorModels[channel] = (IndexColorModel) ip.getColorModel();
-          //}
-
-          // add plane to image stack
-          int w = region.width, h = region.height;
-          if (ip instanceof ByteProcessor) {
-            if (stackB == null) stackB = new ImageStack(w, h);
-            stackB.addSlice(label, ip);
-          }
-          else if (ip instanceof ShortProcessor) {
-            if (stackS == null) stackS = new ImageStack(w, h);
-            stackS.addSlice(label, ip);
-          }
-          else if (ip instanceof FloatProcessor) {
-            // merge image plane into existing stack if possible
-            if (stackB != null) {
-              ip = ip.convertToByte(true);
-              stackB.addSlice(label, ip);
-            }
-            else if (stackS != null) {
-              ip = ip.convertToShort(true);
-              stackS.addSlice(label, ip);
-            }
-            else {
-              if (stackF == null) stackF = new ImageStack(w, h);
-              stackF.addSlice(label, ip);
-            }
-          }
-          else if (ip instanceof ColorProcessor) {
-            if (stackO == null) stackO = new ImageStack(w, h);
-            stackO.addSlice(label, ip);
-          }
-        }
-      }
-
-      notifyListeners(new StatusEvent(1, 1, "Creating image"));
-
-      ImagePlus impB = createImage(stackB, s, fi);
-      ImagePlus impS = createImage(stackS, s, fi);
-      ImagePlus impF = createImage(stackF, s, fi);
-      ImagePlus impO = createImage(stackO, s, fi);
-      if (impB != null) imps.add(impB);
-      if (impS != null) imps.add(impS);
-      if (impF != null) imps.add(impF);
-      if (impO != null) imps.add(impO);
+      readSeries(s, imps);
     }
 
@@ -365 +182 @@
 
     return imps;
+  }
+
+  private long startTime, time;
+  private void startTiming() {
+    startTime = time = System.currentTimeMillis();
+  }
+  private void updateTiming(int s, int i, int current, int total) {
+    ImageProcessorReader reader = process.getReader();
+    long clock = System.currentTimeMillis();
+    if (clock - time >= 100) {
+      String sLabel = reader.getSeriesCount() > 1 ?
+        ("series " + (s + 1) + ", ") : "";
+      String pLabel = "plane " + (i + 1) + "/" + total;
+      notifyListeners(new StatusEvent("Reading " + sLabel + pLabel));
+      time = clock;
+    }
+    notifyListeners(new StatusEvent(current, total, null));
+  }
+
+  private FileInfo createFileInfo() {
+    FileInfo fi = new FileInfo();
+
+    // populate common FileInfo fields
+    String idDir = process.getIdLocation() == null ?
+      null : process.getIdLocation().getParent();
+    if (idDir != null && !idDir.endsWith(File.separator)) {
+      idDir += File.separator;
+    }
+    fi.fileName = process.getIdName();
+    fi.directory = idDir;
+
+    // dump OME-XML to ImageJ's description field, if available
+    try {
+      ServiceFactory factory = new ServiceFactory();
+      OMEXMLService service = factory.getInstance(OMEXMLService.class);
+      fi.description = service.getOMEXML(process.getOMEMetadata());
+    }
+    catch (DependencyException de) { }
+    catch (ServiceException se) { }
+
+    return fi;
+  }
+
+  private void readSeries(int s, List<ImagePlus> imps)
+    throws FormatException, IOException
+  {
+    ImageProcessorReader reader = process.getReader();
+    ImporterOptions options = process.getOptions();
+    reader.setSeries(s);
+
+    boolean[] load = getPlanesToLoad(s);
+    int current = 0, total = 0;
+    for (int j=0; j<reader.getImageCount(); j++) if (load[j]) total++;
+
+    FileInfo fi = createFileInfo();
+
+    ImageStack stackB = null; // for byte images (8-bit)
+    ImageStack stackS = null; // for short images (16-bit)
+    ImageStack stackF = null; // for floating point images (32-bit)
+    ImageStack stackO = null; // for all other images (24-bit RGB)
+
+    Region region = process.getCropRegion(s);
+
+    if (options.isVirtual()) {
+      boolean doMerge = false; //options.isMergeChannels();
+      boolean doColorize = false; //options.isColorize();
+
+      reader.setSeries(s);
+      // NB: ImageJ 1.39+ is required for VirtualStack
+      BFVirtualStack virtualStackB = new BFVirtualStack(options.getId(),
+        reader, doColorize, doMerge, options.isRecord());
+      stackB = virtualStackB;
+      if (doMerge) {
+        for (int j=0; j<reader.getImageCount(); j++) {
+          int[] zct = reader.getZCTCoords(j);
+          if (zct[1] > 0) continue;
+          ChannelMerger channelMerger = new ChannelMerger(reader);
+          int index = channelMerger.getIndex(zct[0], zct[1], zct[2]);
+          String label = constructSliceLabel(index,
+            channelMerger, process.getOMEMetadata(), s,
+            process.getZCount(s), process.getCCount(s), process.getTCount(s));
+          virtualStackB.addSlice(label);
+        }
+      }
+      else {
+        for (int j=0; j<reader.getImageCount(); j++) {
+          String label = constructSliceLabel(j,
+            reader, process.getOMEMetadata(), s,
+            process.getZCount(s), process.getCCount(s), process.getTCount(s));
+          virtualStackB.addSlice(label);
+        }
+      }
+    }
+    else {
+      // CTR CHECK
+      //if (r.isIndexed()) colorModels = new IndexColorModel[r.getSizeC()];
+
+      for (int i=0; i<reader.getImageCount(); i++) {
+        if (!load[i]) continue;
+
+        // limit message update rate
+        updateTiming(s, i, current++, total);
+
+        String label = constructSliceLabel(i,
+          reader, process.getOMEMetadata(), s,
+          process.getZCount(s), process.getCCount(s), process.getTCount(s));
+
+        // get image processor for ith plane
+        ImageProcessor[] p;
+        p = reader.openProcessors(i, region.x, region.y,
+          region.width, region.height);
+        ImageProcessor ip = p[0];
+        if (p.length > 1) {
+          ip = ImagePlusTools.makeRGB(p).getProcessor();
+        }
+        if (ip == null) {
+          throw new FormatException("Cannot read ImageProcessor #" + i);
+        }
+
+        // CTR CHECK
+        //int channel = r.getZCTCoords(i)[1];
+        //if (colorModels != null && p.length == 1) {
+        //  colorModels[channel] = (IndexColorModel) ip.getColorModel();
+        //}
+
+        // add plane to image stack
+        int w = region.width, h = region.height;
+        if (ip instanceof ByteProcessor) {
+          if (stackB == null) stackB = new ImageStack(w, h);
+          stackB.addSlice(label, ip);
+        }
+        else if (ip instanceof ShortProcessor) {
+          if (stackS == null) stackS = new ImageStack(w, h);
+          stackS.addSlice(label, ip);
+        }
+        else if (ip instanceof FloatProcessor) {
+          // merge image plane into existing stack if possible
+          if (stackB != null) {
+            ip = ip.convertToByte(true);
+            stackB.addSlice(label, ip);
+          }
+          else if (stackS != null) {
+            ip = ip.convertToShort(true);
+            stackS.addSlice(label, ip);
+          }
+          else {
+            if (stackF == null) stackF = new ImageStack(w, h);
+            stackF.addSlice(label, ip);
+          }
+        }
+        else if (ip instanceof ColorProcessor) {
+          if (stackO == null) stackO = new ImageStack(w, h);
+          stackO.addSlice(label, ip);
+        }
+      }
+    }
+
+    notifyListeners(new StatusEvent(1, 1, "Creating image"));
+
+    ImagePlus impB = createImage(stackB, s, fi);
+    ImagePlus impS = createImage(stackS, s, fi);
+    ImagePlus impF = createImage(stackF, s, fi);
+    ImagePlus impO = createImage(stackO, s, fi);
+    if (impB != null) imps.add(impB);
+    if (impS != null) imps.add(impS);
+    if (impF != null) imps.add(impF);
+    if (impO != null) imps.add(impO);
+  }
+
+  private boolean[] getPlanesToLoad(int s) {
+    ImageProcessorReader reader = process.getReader();
+    boolean[] load = new boolean[reader.getImageCount()];
+    int cBegin = process.getCBegin(s);
+    int cEnd = process.getCEnd(s);
+    int cStep = process.getCStep(s);
+    int zBegin = process.getZBegin(s);
+    int zEnd = process.getZEnd(s);
+    int zStep = process.getZStep(s);
+    int tBegin = process.getTBegin(s);
+    int tEnd = process.getTEnd(s);
+    int tStep = process.getTStep(s);
+    for (int c=cBegin; c<=cEnd; c+=cStep) {
+      for (int z=zBegin; z<=zEnd; z+=zStep) {
+        for (int t=tBegin; t<=tEnd; t+=tStep) {
+          //int index = r.isOrderCertain() ? r.getIndex(z, c, t) : c;
+          int index = reader.getIndex(z, c, t);
+          load[index] = true;
+        }
+      }
+    }
+    return load;
   }
 
@@ -453 +461 @@
 //          stackOrder, lut, r.getSeries(), null, hyper);
 //      }
-//
-//      // CTR FIXME
-//      if (splitC || splitZ || splitT) {
-//        imp = Slicer.reslice(imp, splitC, splitZ, splitT, hyper, stackOrder);
-//      }
 //    }
 
@@ -493 +496 @@
   }
 
-  /** Constructs slice label. */
   private String constructSliceLabel(int ndx, IFormatReader r,
     IMetadata meta, int series, int zCount, int cCount, int tCount)

trunk/components/loci-plugins/src/loci/plugins/in/ImportProcess.java

@@ -154 +154 @@
     initializeCrop();
 
+    step(ImportStep.COLORS);
+    if (cancel) return false;
+    initializeColors();
+
     step(ImportStep.METADATA);
     if (cancel) return false;
@@ -305 +309 @@
   public Region getCropRegion(int s) {
     assertStep(ImportStep.STACK);
-    Region region = options.getCropRegion(s);
-    if (region != null) return region;
+    Region region = options.doCrop() ? options.getCropRegion(s) : null;
     ImageProcessorReader r = getReader();
-    return new Region(0, 0, r.getSizeX(), r.getSizeY());
+    int sizeX = r.getSizeX(), sizeY = r.getSizeY();
+    if (region == null) {
+      // entire image plane is the default region
+      region = new Region(0, 0, sizeX, sizeY);
+    }
+    else {
+      // bounds checking for cropped region
+      if (region.x < 0) region.x = 0;
+      if (region.y < 0) region.y = 0;
+      if (region.width <= 0 || region.x + region.width > sizeX) {
+        region.width = sizeX - region.x;
+      }
+      if (region.height <= 0 || region.y + region.height > sizeY) {
+        region.height = sizeX - region.y;
+      }
+    }
+    return region;
   }
 
@@ -457 +476 @@
   /** Performed following ImportStep.CROP notification. */
   private void initializeCrop() { }
+
+  /** Performed following ImportStep.COLORS notification. */
+  private void initializeColors() { }
 
   /** Performed following ImportStep.METADATA notification. */

trunk/components/loci-plugins/src/loci/plugins/in/ImportStep.java

@@ -46 +46 @@
   RANGE     (5, "Confirming planar ranges"),
   CROP      (6, "Confirming crop region"),
-  METADATA  (7, "Initializing metadata"),
-  COMPLETE  (8, "Import preparations complete");
+  COLORS    (7, "Confirming colorization"),
+  METADATA  (8, "Initializing metadata"),
+  COMPLETE  (9, "Import preparations complete");
 
   // -- Static fields --

trunk/components/loci-plugins/src/loci/plugins/in/ImporterOptions.java

@@ -26 +26 @@
 package loci.plugins.in;
 
+import java.awt.Color;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -132 +133 @@
   private List<Region> cropRegion = new ArrayList<Region>();
 
+  // color mode options
+  private List<List<Color>> customColors = new ArrayList<List<Color>>();
+
   // -- Constructor --
 
@@ -396 +400 @@
   public void setCropRegion(int s, Region r) { set(cropRegion, s, r, null); }
 
+  // color mode options
+  public Color getCustomColor(int s, int c) {
+    List<Color> list = get(customColors, s, null);
+    if (list == null) return null;
+    return get(list, c, null);
+  }
+  public void setCustomColor(int s, int c, Color color) {
+    List<Color> list = get(customColors, s, null);
+    if (list == null) {
+      list = new ArrayList<Color>();
+      set(customColors, s, list, null);
+    }
+    set(list, c, color, null);
+  }
+
   // -- Helper methods - miscellaneous --
 

trunk/components/loci-plugins/src/loci/plugins/in/ImporterPrompter.java

@@ -94 +94 @@
         if (!promptCrop()) process.cancel();
         break;
+      case COLORS:
+        if (!promptColors()) process.cancel();
+        break;
       case METADATA:
         break;
@@ -153 +156 @@
     return dialog.showDialog() == OptionsDialog.STATUS_OK;
   }
-  
+
+  /** Prompts for color details, if necessary. */
+  private boolean promptColors() {
+    ColorDialog dialog = new ColorDialog(process);
+    return dialog.showDialog() == OptionsDialog.STATUS_OK;
+  }
 }