Added exception for converter from grayscale image

Task: #284 (http://github.com/CellDynamics/QuimP/issues/284)

src/main/java/com/github/celldynamics/quimp/plugin/randomwalk/PropagateSeeds.java

@@ -539,7 +539,7 @@ public Contour(boolean storeSeeds, AutoThresholder.Method trueBackground, double
     public Seeds propagateSeed(ImageProcessor previous, ImageProcessor org, double shrinkPower,
             double expandPower) {
       // FIXME if there are two separate objects in the same color they will be treated as
-      // separately
+      // separate objects
       double stepsshrink = shrinkPower / stepSize; // total shrink/step size
       double stepsexp = (expandPower) / stepSize; // total shrink/step size
       Seeds ret = new Seeds(2);
@@ -676,37 +676,42 @@ public Seeds propagateSeed(ImageProcessor previous, ImageProcessor org, double s
       // store seeds if option ticked
       Seeds ret = new Seeds(2);
       // need to process each object separately to preserve multi fg seeds.
-      Seeds decodedSeeds = SeedProcessor.getGrayscaleAsSeeds(cp);
-      for (ImageProcessor ip : decodedSeeds.get(SeedTypes.FOREGROUNDS)) {
-        // make objects smaller
-        small = BinaryFilters.iterateMorphological(ip, MorphoOperations.ERODE, shrinkPower);
-        ret.put(SeedTypes.FOREGROUNDS, small);
-      }
+      Seeds decodedSeeds;
+      try {
+        decodedSeeds = SeedProcessor.getGrayscaleAsSeeds(cp);
+        for (ImageProcessor ip : decodedSeeds.get(SeedTypes.FOREGROUNDS)) {
+          // make objects smaller
+          small = BinaryFilters.iterateMorphological(ip, MorphoOperations.ERODE, shrinkPower);
+          ret.put(SeedTypes.FOREGROUNDS, small);
+        }
 
-      // make background bigger but for all, convert to binary first
-      big.threshold(0);
-      big = BinaryFilters.iterateMorphological(big, MorphoOperations.DILATE, expandPower);
-      cp.threshold(0); // input also must be binary (after computing FG)
-
-      // apply big to old background making object bigger and prevent covering objects on
-      // frame
-      // n+1
-      // by previous background (make "empty" not seeded space around objects)
-      // IJ.saveAsTiff(new ImagePlus("", big), "/tmp/testIterateMorphological_bigbef.tif");
-      // IJ.saveAsTiff(new ImagePlus("", cp), "/tmp/testIterateMorphological_cp.tif");
-      for (int x = 0; x < cp.getWidth(); x++) {
-        for (int y = 0; y < cp.getHeight(); y++) {
-          big.putPixel(x, y, big.getPixel(x, y) | cp.getPixel(x, y));
+        // make background bigger but for all, convert to binary first
+        big.threshold(0);
+        big = BinaryFilters.iterateMorphological(big, MorphoOperations.DILATE, expandPower);
+        cp.threshold(0); // input also must be binary (after computing FG)
+
+        // apply big to old background making object bigger and prevent covering objects on
+        // frame
+        // n+1
+        // by previous background (make "empty" not seeded space around objects)
+        // IJ.saveAsTiff(new ImagePlus("", big), "/tmp/testIterateMorphological_bigbef.tif");
+        // IJ.saveAsTiff(new ImagePlus("", cp), "/tmp/testIterateMorphological_cp.tif");
+        for (int x = 0; x < cp.getWidth(); x++) {
+          for (int y = 0; y < cp.getHeight(); y++) {
+            big.putPixel(x, y, big.getPixel(x, y) | cp.getPixel(x, y));
+          }
         }
-      }
 
-      big.invert(); // invert to have BG pixels white in seed. (required by convertToList)
+        big.invert(); // invert to have BG pixels white in seed. (required by convertToList)
 
-      ret.put(SeedTypes.BACKGROUND, getTrueBackground(big, org));
-      if (storeSeeds) {
-        seeds.add(ret);
+        ret.put(SeedTypes.BACKGROUND, getTrueBackground(big, org));
+        if (storeSeeds) {
+          seeds.add(ret);
+        }
+      } catch (RandomWalkException e) { // from decodeseeds - no FG seeds
+        // this is handled to console only as return is still valid (no FG seeds in output)
+        LOGGER.debug("Empty seeds.");
       }
-
       return ret;
     }
 

src/main/java/com/github/celldynamics/quimp/plugin/randomwalk/RandomWalkSegmentation.java

@@ -305,15 +305,19 @@ private enum StoppedBy {
   public enum SeedTypes {
     /**
      * Denote foreground related data. Usually on index 0.
+     * 
+     * <p>FG data can be grayscale images up to 8-bits.
      */
     FOREGROUNDS(0),
     /**
      * Denote background related data. Usually on index 1.
+     * 
+     * <p>BG data can be grayscale image up to 8-bits.
      */
     BACKGROUND(1),
     /**
      * Rough mask used for computing local mean. Used only if {@link RandomWalkOptions#useLocalMean}
-     * is true.
+     * is true. This mask should be always binary.
      * 
      * @see RandomWalkSegmentation#solver(Seeds, RealMatrix[])
      * @see RandomWalkSegmentation#getMeanSeedLocal(ImageProcessor, int)
@@ -443,7 +447,7 @@ public ImageProcessor run(Seeds seeds) throws RandomWalkException {
       }
       solved = solver(seedsNext, precomputed);
     }
-    RealMatrix result = compare(solved); // result as matrix // FIXME can be null
+    RealMatrix result = compare(solved); // result as matrix
     ImageProcessor resultim = realMatrix2ImageProcessor(result).convertToByteProcessor(true);
     // cut mask - cut segmentation result by initial ROUGHMASK if present
     if (params.maskLimit == true && seeds.get(SeedTypes.ROUGHMASK) != null) {
@@ -1042,7 +1046,7 @@ protected ProbabilityMaps solver(Seeds seeds, RealMatrix[] gradients) {
 
       // get average "distance" between weights multiplying w = w.*avgw, this is only for
       // optimisation purposes.
-      // does not apply for FG if we use local mean, applied for BG always FIXME why?
+      // does not apply for FG if we use local mean, applied for BG always (better results)
       if (params.useLocalMean == false || userBckPoints.contains(seedsPointsFg.get(cell))) {
         wrfg.walkInOptimizedOrder(new MatrixDotProduct(avgwxfg));
         wlfg.walkInOptimizedOrder(new MatrixDotProduct(avgwxfg));

src/main/java/com/github/celldynamics/quimp/plugin/randomwalk/RandomWalkSegmentationPlugin_.java

@@ -797,7 +797,6 @@ public ImagePlus runPlugin() {
           foreColor = Color.RED;
           backColor = Color.GREEN;
           if (seedImage.getNSlices() >= startSlice) {
-            // FIXME seeds can be empty (but at least one map will exist always)
             seeds = SeedProcessor.decodeSeedsfromRgb(seedImage.getStack().getProcessor(startSlice),
                     Arrays.asList(foreColor), backColor);
           } else {
@@ -825,6 +824,10 @@ public ImagePlus runPlugin() {
           if (seedImage == null) {
             throw new RandomWalkException("Mask image could not be loaded");
           }
+          // TODO add checkbox in UI to show (in QCONFfile dynamic region)
+          ImagePlus maskToDisplay = seedImage.duplicate();
+          maskToDisplay.setTitle("Mask-" + Paths.get(model.qconfFile).getFileName().toString());
+          maskToDisplay.show();
           // TODO check if each slice max value is less than 255
           // and continue to the next case
         case MaskImage:
@@ -835,7 +838,7 @@ public ImagePlus runPlugin() {
                   is.getProcessor(startSlice), model.shrinkPower, model.expandPower);
           // mask to local mean
           seeds.put(SeedTypes.ROUGHMASK,
-                  seedImage.getStack().getProcessor(startSlice).convertToByte(true).duplicate());
+                  seedImage.getStack().getProcessor(startSlice).convertToByte(true));
           seeds.get(SeedTypes.ROUGHMASK, 1).threshold(0); // to have BW map in case
           break;
         default:
@@ -878,7 +881,8 @@ public ImagePlus runPlugin() {
                       seedImage.getStack().getProcessor(s).convertToByte(true), is.getProcessor(s),
                       model.shrinkPower, model.expandPower);
               nextseed.put(SeedTypes.ROUGHMASK,
-                      seedImage.getStack().getProcessor(s).convertToByte(false));
+                      seedImage.getStack().getProcessor(s).convertToByte(false)); // this makes copy
+              nextseed.get(SeedTypes.ROUGHMASK, 1).threshold(0); // to have BW map in case
               break;
             default:
           }

src/main/java/com/github/celldynamics/quimp/plugin/randomwalk/SeedProcessor.java

@@ -283,8 +283,9 @@ public static ImageProcessor flatten(Seeds seeds, SeedTypes type, int initialVal
    * 
    * @param im 8-bit grayscale image, 0 is background
    * @return Seeds with {@link SeedTypes#FOREGROUNDS} filled. No {@link SeedTypes#BACKGROUND}
+   * @throws RandomWalkException when all output FG seed maps are empty
    */
-  public static Seeds getGrayscaleAsSeeds(ImageProcessor im) {
+  public static Seeds getGrayscaleAsSeeds(ImageProcessor im) throws RandomWalkException {
     Seeds ret = new Seeds(2);
     ImageStatistics stats = im.getStats();
     int max = (int) stats.max; // max value
@@ -316,6 +317,7 @@ public static Seeds getGrayscaleAsSeeds(ImageProcessor im) {
         ret.get(SeedTypes.FOREGROUNDS).remove(i.intValue() - 1);
       }
     }
+    validateSeeds(ret, SeedTypes.FOREGROUNDS);
     return ret;
   }
 

src/main/java/com/github/celldynamics/quimp/plugin/randomwalk/Seeds.java

@@ -28,9 +28,11 @@
  * in {@link ImageStack}. One needs to take care about proper unwrapping data if standard
  * {@link #get(Object)} is used.
  * 
+ * <p>Seed maps can be converted from various sources like RGB images or grayscale images but maps
+ * are always binary.
  * 
  * @author p.baniukiewicz
- *
+ * @see SeedProcessor
  */
 @SuppressWarnings("serial")
 public class Seeds extends ListMap<ImageProcessor> {