Updated for Icy kernel 2.4.0 (interruptible process)

pom.xml

@@ -11,7 +11,7 @@
     </parent>
 
     <artifactId>protocols</artifactId>
-    <version>3.2.1</version>
+    <version>3.2.2</version>
 
     <packaging>jar</packaging>
 

src/main/java/plugins/adufour/blocks/tools/ij/ImagePlusToSequence.java

@@ -5,28 +5,44 @@ import icy.plugin.abstract_.Plugin;
 import plugins.adufour.blocks.util.VarList;
 import plugins.adufour.vars.lang.VarImagePlus;
 import plugins.adufour.vars.lang.VarSequence;
+import plugins.adufour.vars.util.VarException;
 
 public class ImagePlusToSequence extends Plugin implements IJBlock
 {
     VarImagePlus vip = new VarImagePlus("IJ ImagePlus", null);
-    VarSequence  vs  = new VarSequence("Icy Sequence", null);
-    
+    VarSequence vs = new VarSequence("Icy Sequence", null);
+
     @Override
     public void run()
     {
-        vs.setValue(ImageJUtil.convertToIcySequence(vip.getValue(true), null));
+        try
+        {
+            vs.setValue(ImageJUtil.convertToIcySequence(vip.getValue(true), null));
+        }
+        catch (IllegalAccessError e)
+        {
+            throw new VarException(vip, e.getMessage());
+        }
+        catch (VarException e)
+        {
+            throw e;
+        }
+        catch (InterruptedException e)
+        {
+            Thread.currentThread().interrupt();
+        }
     }
-    
+
     @Override
     public void declareInput(VarList inputMap)
     {
         inputMap.add("IJ ImagePlus", vip);
     }
-    
+
     @Override
     public void declareOutput(VarList outputMap)
     {
         outputMap.add("Icy Sequence", vs);
     }
-    
+
 }

src/main/java/plugins/adufour/blocks/tools/ij/SequenceToImagePlus.java

@@ -5,6 +5,7 @@ import icy.plugin.abstract_.Plugin;
 import plugins.adufour.blocks.util.VarList;
 import plugins.adufour.vars.lang.VarImagePlus;
 import plugins.adufour.vars.lang.VarSequence;
+import plugins.adufour.vars.util.VarException;
 
 public class SequenceToImagePlus extends Plugin implements IJBlock
 {
@@ -14,7 +15,22 @@ public class SequenceToImagePlus extends Plugin implements IJBlock
     @Override
     public void run()
     {
-        vip.setValue(ImageJUtil.convertToImageJImage(vs.getValue(true), null));
+        try
+        {
+            vip.setValue(ImageJUtil.convertToImageJImage(vs.getValue(true), null));
+        }
+        catch (IllegalAccessError e)
+        {
+            throw new VarException(vs, e.getMessage());
+        }
+        catch (VarException e)
+        {
+            throw e;
+        }
+        catch (InterruptedException e)
+        {
+            Thread.currentThread().interrupt();
+        }
     }
     
     @Override

src/main/java/plugins/adufour/blocks/tools/roi/DilateROI.java

@@ -24,16 +24,23 @@ public class DilateROI extends MorphROI
     @Override
     public void run()
     {
-        switch (unit.getValue())
+        try
         {
-            case PIXELS:
-                roiOUT.setValue(dilateROI(roiIN.getValue(), x.getValue(), y.getValue(), z.getValue()));
-                break;
-            case PERCENTAGE:
-                roiOUT.setValue(dilateROIByPercentage(roiIN.getValue(), x.getValue(), y.getValue(), z.getValue()));
-                break;
-            default:
-                throw new VarException(unit, "Unsupported unit");
+            switch (unit.getValue())
+            {
+                case PIXELS:
+                    roiOUT.setValue(dilateROI(roiIN.getValue(), x.getValue(), y.getValue(), z.getValue()));
+                    break;
+                case PERCENTAGE:
+                    roiOUT.setValue(dilateROIByPercentage(roiIN.getValue(), x.getValue(), y.getValue(), z.getValue()));
+                    break;
+                default:
+                    throw new VarException(unit, "Unsupported unit");
+            }
+        }
+        catch (InterruptedException e)
+        {
+            Thread.currentThread().interrupt();
         }
     }
 
@@ -50,8 +57,9 @@ public class DilateROI extends MorphROI
      * @param zRadius
      *        the radius (in pixels) along Z (not used if <code>roi</code> is 2D)
      * @return a new set of dilated ROI of type "area"
+     * @throws InterruptedException
      */
-    public static ROI[] dilateROI(ROI[] inputRoi, int xRadius, int yRadius, int zRadius)
+    public static ROI[] dilateROI(ROI[] inputRoi, int xRadius, int yRadius, int zRadius) throws InterruptedException
     {
         ArrayList<ROI> out = new ArrayList<ROI>(inputRoi.length);
 
@@ -81,8 +89,9 @@ public class DilateROI extends MorphROI
      * @param zPct
      *        the percentage (from 0 to 100) to dilate along Z (not used in 2D)
      * @return a new set of dilated ROI of type "area"
+     * @throws InterruptedException
      */
-    public static ROI[] dilateROIByPercentage(ROI[] inputRoi, int xPct, int yPct, int zPct)
+    public static ROI[] dilateROIByPercentage(ROI[] inputRoi, int xPct, int yPct, int zPct) throws InterruptedException
     {
         ArrayList<ROI> out = new ArrayList<ROI>(inputRoi.length);
 
@@ -113,8 +122,9 @@ public class DilateROI extends MorphROI
      * @param zPct
      *        the percentage (from 0 to 100) to dilate along Z (not used in 2D)
      * @return a new, dilated ROI of type "area"
+     * @throws InterruptedException
      */
-    public static ROI dilateROIByPercentage(ROI roi, int xPct, int yPct, int zPct)
+    public static ROI dilateROIByPercentage(ROI roi, int xPct, int yPct, int zPct) throws InterruptedException
     {
         int xRadius = percentageToRadiusX(roi, xPct);
         int yRadius = percentageToRadiusY(roi, yPct);
@@ -135,8 +145,9 @@ public class DilateROI extends MorphROI
      * @param zRadius
      *        the radius in pixels along Z (not used if <code>roi</code> is 2D)
      * @return a new, dilated ROI of type "area"
+     * @throws InterruptedException
      */
-    public static ROI dilateROI(ROI roi, int xRadius, int yRadius, int zRadius)
+    public static ROI dilateROI(ROI roi, int xRadius, int yRadius, int zRadius) throws InterruptedException
     {
         int rx = xRadius, rrx = rx * rx;
         int ry = yRadius, rry = ry * ry;

src/main/java/plugins/adufour/blocks/tools/roi/ErodeROI.java

@@ -24,16 +24,23 @@ public class ErodeROI extends MorphROI
     @Override
     public void run()
     {
-        switch (unit.getValue())
+        try
         {
-            case PIXELS:
-                roiOUT.setValue(erodeROI(roiIN.getValue(), x.getValue(), y.getValue(), z.getValue()));
-                break;
-            case PERCENTAGE:
-                roiOUT.setValue(erodeROIByPercentage(roiIN.getValue(), x.getValue(), y.getValue(), z.getValue()));
-                break;
-            default:
-                throw new VarException(unit, "Unsupported unit");
+            switch (unit.getValue())
+            {
+                case PIXELS:
+                    roiOUT.setValue(erodeROI(roiIN.getValue(), x.getValue(), y.getValue(), z.getValue()));
+                    break;
+                case PERCENTAGE:
+                    roiOUT.setValue(erodeROIByPercentage(roiIN.getValue(), x.getValue(), y.getValue(), z.getValue()));
+                    break;
+                default:
+                    throw new VarException(unit, "Unsupported unit");
+            }
+        }
+        catch (InterruptedException e)
+        {
+            Thread.currentThread().interrupt();
         }
     }
 
@@ -50,8 +57,9 @@ public class ErodeROI extends MorphROI
      * @param zRadius
      *        the radius (in pixels) along Z (not used if <code>roi</code> is 2D)
      * @return a new set of eroded ROI of type "area"
+     * @throws InterruptedException
      */
-    public static ROI[] erodeROI(ROI[] inputRoi, int xRadius, int yRadius, int zRadius)
+    public static ROI[] erodeROI(ROI[] inputRoi, int xRadius, int yRadius, int zRadius) throws InterruptedException
     {
         ArrayList<ROI> out = new ArrayList<ROI>(inputRoi.length);
 
@@ -81,8 +89,9 @@ public class ErodeROI extends MorphROI
      * @param zPct
      *        the percentage (from 0 to 100) to erode along Z (not used in 2D)
      * @return a new set of eroded ROI of type "area"
+     * @throws InterruptedException
      */
-    public static ROI[] erodeROIByPercentage(ROI[] inputRoi, int xPct, int yPct, int zPct)
+    public static ROI[] erodeROIByPercentage(ROI[] inputRoi, int xPct, int yPct, int zPct) throws InterruptedException
     {
         ArrayList<ROI> out = new ArrayList<ROI>(inputRoi.length);
 
@@ -113,8 +122,9 @@ public class ErodeROI extends MorphROI
      * @param zPct
      *        the percentage (from 0 to 100) to dilate along Z (not used in 2D)
      * @return a new, dilated ROI of type "area"
+     * @throws InterruptedException
      */
-    public static ROI erodeROIByPercentage(ROI roi, int xPct, int yPct, int zPct)
+    public static ROI erodeROIByPercentage(ROI roi, int xPct, int yPct, int zPct) throws InterruptedException
     {
         int xRadius = percentageToRadiusX(roi, xPct);
         int yRadius = percentageToRadiusY(roi, yPct);
@@ -135,8 +145,9 @@ public class ErodeROI extends MorphROI
      * @param zRadius
      *        the radius in pixels along Z (not used if <code>roi</code> is 2D)
      * @return a new, eroded ROI of type "area"
+     * @throws InterruptedException
      */
-    public static ROI erodeROI(ROI roi, int xRadius, int yRadius, int zRadius)
+    public static ROI erodeROI(ROI roi, int xRadius, int yRadius, int zRadius) throws InterruptedException
     {
         // The basis of this erosion operator is to remove all pixels within a distance of "radius"
         // from the border. Since we have easy access to the contour points of the ROI, we will

src/main/java/plugins/adufour/blocks/tools/roi/MergeROI.java

@@ -14,34 +14,40 @@ import plugins.adufour.vars.lang.VarROIArray;
 public class MergeROI extends Plugin implements ROIBlock
 {
     VarEnum<BooleanOperator> operation = new VarEnum<BooleanOperator>("Merge operation", BooleanOperator.AND);
-    
-    VarROIArray              roiIn     = new VarROIArray("List of ROI");
-    
-    VarROIArray              roiOut    = new VarROIArray("Merged ROI");
-    
+
+    VarROIArray roiIn = new VarROIArray("List of ROI");
+
+    VarROIArray roiOut = new VarROIArray("Merged ROI");
+
     @Override
     public void run()
     {
         roiOut.setValue(new ROI[0]);
-        
-        List<ROI> rois = Arrays.asList(roiIn.getValue());
-        
-        ROI merge = ROIUtil.merge(rois, operation.getValue());
-        
-        if (merge != null) roiOut.add(merge);
+
+        try
+        {
+            List<ROI> rois = Arrays.asList(roiIn.getValue());
+            ROI merge = ROIUtil.merge(rois, operation.getValue());
+            if (merge != null)
+                roiOut.add(merge);
+        }
+        catch (InterruptedException e)
+        {
+            Thread.currentThread().interrupt();
+        }
     }
-    
+
     @Override
     public void declareInput(VarList inputMap)
     {
         inputMap.add("List of ROI", roiIn);
         inputMap.add("Merge operation", operation);
     }
-    
+
     @Override
     public void declareOutput(VarList outputMap)
     {
         outputMap.add("Merged ROI", roiOut);
     }
-    
+
 }

src/main/java/plugins/adufour/blocks/tools/roi/SubtractROI.java

@@ -18,7 +18,14 @@ public class SubtractROI extends Plugin implements ROIBlock
     @Override
     public void run()
     {
-        roiOut.setValue(subtractROI(roiA.getValue(true), roiB.getValue(true)));
+        try
+        {
+            roiOut.setValue(subtractROI(roiA.getValue(true), roiB.getValue(true)));
+        }
+        catch (InterruptedException e)
+        {
+            Thread.currentThread().interrupt();
+        }
     }
 
     @Override
@@ -42,8 +49,10 @@ public class SubtractROI extends Plugin implements ROIBlock
      * @param roiB
      *        ROIs subtracted from the first group of ROIs.
      * @return A - B. The group of ROIs resulting from the subtraction from the each element of the group A and each element of the group B.
+     * @throws InterruptedException
+     * @throws UnsupportedOperationException
      */
-    public static ROI[] subtractROI(ROI[] roiA, ROI[] roiB)
+    public static ROI[] subtractROI(ROI[] roiA, ROI[] roiB) throws UnsupportedOperationException, InterruptedException
     {
         ArrayList<ROI> out = new ArrayList<ROI>(roiA.length);
 

src/main/java/plugins/adufour/blocks/tools/sequence/SequenceScreenshot.java

@@ -44,11 +44,21 @@ public class SequenceScreenshot extends Plugin implements SequenceBlock
 
         final Canvas2D canvas2D = canvas2DP[0];
 
-        for (int t = 0; t < time; t++)
-            for (int z = 0; z < depth; z++)
-                out.setImage(t, z, canvas2D.getRenderedImage(t, z, -1, false));
-
-        viewer.close();
+        try
+        {
+            for (int t = 0; t < time; t++)
+                for (int z = 0; z < depth; z++)
+                    out.setImage(t, z, canvas2D.getRenderedImage(t, z, -1, false));
+        }
+        catch (InterruptedException e)
+        {
+            Thread.currentThread().interrupt();
+            return;
+        }
+        finally
+        {
+            viewer.close();
+        }
 
         seqOut.setValue(out);
     }