First implementation of watershed block

.gitignore

@@ -3,9 +3,11 @@
 bin/
 build/
 target/
+workspace/
 *.iml
 *.eml
 *.jar
 .classpath
 .project
 export.jardesc
+setting.xml

src/main/java/plugins/stef/roi/bloc/RoiBlocks.java

 package plugins.stef.roi.bloc;
 
+import icy.main.Icy;
+import icy.plugin.PluginDescriptor;
+import icy.plugin.PluginLauncher;
+import icy.plugin.PluginLoader;
 import icy.plugin.abstract_.Plugin;
 import icy.plugin.interface_.PluginLibrary;
+import plugins.adufour.protocols.Protocols;
 
 /**
  * Bundle of blocks (Protocols) to perform different operations on ROI (Region Of Interest).<br>
@@ -21,5 +26,10 @@ import icy.plugin.interface_.PluginLibrary;
  */
 public class RoiBlocks extends Plugin implements PluginLibrary
 {
-    //
+
+    public static void main(String[] args)
+    {
+        Icy.main(args);
+        PluginLauncher.start(PluginLoader.getPlugin(Protocols.class.getName()));
+    }
 }

src/main/java/plugins/stef/roi/bloc/op/SeparateROIWatershed.java

+/**
+ * 
+ */
+package plugins.stef.roi.bloc.op;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import icy.plugin.abstract_.Plugin;
+import icy.plugin.interface_.PluginBundled;
+import icy.plugin.interface_.PluginLibrary;
+import icy.roi.ROI;
+import icy.roi.ROIUtil;
+import icy.system.IcyHandledException;
+import icy.type.dimension.Dimension3D;
+import icy.type.dimension.Dimension5D;
+import icy.type.rectangle.Rectangle5D;
+import plugins.adufour.blocks.tools.roi.ROIBlock;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.stef.roi.bloc.RoiBlocks;
+
+/**
+ * This block allows users to use the watershed separation function available on the ROI tools on the ribbon of Icy.
+ * ROIs are supposed to be 2D ROIs.
+ * Seed ROIs are optional. If no seeds are provided, they will be computed using a distance map on the image.
+ * The result ROIs will be the separated components.
+ * The result seed ROIs will be either the input seeds or the ones computed by the algorithm.
+ * 
+ * @author Daniel Felipe Gonzalez Obando
+ */
+public class SeparateROIWatershed extends Plugin implements ROIBlock, PluginLibrary, PluginBundled
+{
+    protected VarROIArray varInTargetRois;
+    protected VarROIArray varInSeedRois;
+
+    @Override
+    public void declareInput(VarList inputMap)
+    {
+        varInTargetRois = new VarROIArray("ROI(s)");
+        varInSeedRois = new VarROIArray("Seed ROI(s)");
+        inputMap.add("inputRois", varInTargetRois);
+        inputMap.add("inputSeeds", varInSeedRois);
+    }
+
+    protected VarROIArray varOutRois;
+    protected VarROIArray varOutSeeds;
+
+    @Override
+    public void declareOutput(VarList outputMap)
+    {
+        varOutRois = new VarROIArray("Separated ROI(s)");
+        varOutSeeds = new VarROIArray("Seed ROI(s)");
+        outputMap.add("outputRois", varOutRois);
+        outputMap.add("outputSeeds", varOutSeeds);
+    }
+
+    @Override
+    public void run()
+    {
+        final ROI[] rois = varInTargetRois.getValue();
+        final ROI[] seeds = varInSeedRois.getValue();
+        List<ROI> result = new ArrayList<ROI>();
+        List<ROI> seedList;
+        if (rois != null)
+        {
+            try
+            {
+                if (seeds != null && seeds.length > 0)
+                {
+                    seedList = Arrays.asList(seeds);
+                    result = ROIUtil.computeWatershedSeparation(Arrays.asList(rois), seedList, getDimensionSize(rois),
+                            new Dimension3D.Double(1d, 1d, 1d));
+                }
+                else
+                {
+                    seedList = new ArrayList<ROI>();
+                    result = ROIUtil.computeWatershedSeparation(Arrays.asList(rois), getDimensionSize(rois),
+                            new Dimension3D.Double(1d, 1d, 1d), seedList);
+                }
+
+            }
+            catch (Exception e)
+            {
+                throw new IcyHandledException("Error on watershed separation: " + e.getMessage(), e);
+            }
+
+            varOutRois.setValue(result.toArray(new ROI[result.size()]));
+            varOutSeeds.setValue(seedList.toArray(new ROI[seedList.size()]));
+        }
+    }
+
+    private Dimension5D getDimensionSize(ROI[] rois)
+    {
+        Dimension5D.Double dims = new Dimension5D.Double();
+        for (ROI roi : rois)
+        {
+            Rectangle5D roiBounds = roi.getBounds5D();
+            dims.sizeX = Math.max(dims.sizeX, roiBounds.getMaxX() + 10);
+            dims.sizeY = Math.max(dims.sizeY, roiBounds.getMaxY() + 10);
+            dims.sizeZ = Math.max(dims.sizeZ, roiBounds.getMaxZ());
+            dims.sizeT = Math.max(dims.sizeT, roiBounds.getMaxT());
+            dims.sizeC = Math.max(dims.sizeC, roiBounds.getMaxC());
+        }
+
+        if (!Double.isFinite(dims.sizeX) || dims.sizeX == 0)
+            dims.sizeX = 1;
+        if (!Double.isFinite(dims.sizeY) || dims.sizeY == 0)
+            dims.sizeY = 1;
+        if (!Double.isFinite(dims.sizeZ) || dims.sizeZ == 0)
+            dims.sizeZ = 1;
+        if (!Double.isFinite(dims.sizeT) || dims.sizeT == 0)
+            dims.sizeT = 1;
+        if (!Double.isFinite(dims.sizeC) || dims.sizeC == 0)
+            dims.sizeC = 1;
+
+        return dims;
+    }
+
+    @Override
+    public String getMainPluginClassName()
+    {
+        return RoiBlocks.class.getName();
+    }
+
+}