Coordinates saving functionality and some UI alignments. Done by Nikhil.

svn path=/; revision=342

diff --git a/Annotation/src/ie/dcu/apps/ist/PainterRegistry.java b/Annotation/src/ie/dcu/apps/ist/PainterRegistry.java
index 7b437b019b7cb50c03df6829882234733e74aecb..ed5d6fca2959ea558a4e03491f7f551af3c2cde2 100644 (file)
--- a/Annotation/src/ie/dcu/apps/ist/PainterRegistry.java
+++ b/Annotation/src/ie/dcu/apps/ist/PainterRegistry.java
@@ -16,10 +16,13 @@ public class PainterRegistry {
        private void init() {
                add(new CombinedPainter());
                add(new OriginalPainter());
-               add(new MarkupPainter());
-               add(new MaskPainter());
-               add(new ForegroundOnlyPainter());
-               add(new OutlineOverlayPainter());
+               /*
+                * Commented different views of segmentation. Currently original and combined painter are enabled
+                */
+               //add(new MarkupPainter());
+               //add(new MaskPainter());
+               //add(new ForegroundOnlyPainter());
+               //add(new OutlineOverlayPainter());
        }
        
        

diff --git a/Annotation/src/ie/dcu/apps/ist/views/SegmentationView.java b/Annotation/src/ie/dcu/apps/ist/views/SegmentationView.java
index 9e0d223ec4d9399ba284cfb5515a7b1700fbd932..7bd57665c9279276db5e15e26f20e82505ceba7c 100644 (file)
--- a/Annotation/src/ie/dcu/apps/ist/views/SegmentationView.java
+++ b/Annotation/src/ie/dcu/apps/ist/views/SegmentationView.java
@@ -210,7 +210,7 @@ public class SegmentationView extends Composite {
        private void createToolMainToolbar() {
                ToolBarManager m = new ToolBarManager(mainToolbar);
                m.add(getAction(Tool.Foreground));
-               m.add(getAction(Tool.Background));
+               //m.add(getAction(Tool.Background));
                m.add(getAction(Tool.OperatingMode));
                m.add(getAction(Tool.FormSegment));
                m.add(new Separator());

diff --git a/Annotation/src/ie/dcu/segment/SegmentationContext.java b/Annotation/src/ie/dcu/segment/SegmentationContext.java
index 4d4e21e425a88eefbc75721cc84f9f1db35c4af6..89ea60002191437109a7fbcf2a0d4290571b6a29 100644 (file)
--- a/Annotation/src/ie/dcu/segment/SegmentationContext.java
+++ b/Annotation/src/ie/dcu/segment/SegmentationContext.java
@@ -215,10 +215,13 @@ public class SegmentationContext {
                
        public static void disableAllSegments()
        {
-               for(SegmentationMask currentSegmentMask : segmentationMaskObjects)
+               if (!(segmentationMaskObjects.isEmpty()))
                {
-                       currentSegmentMask.enabled = false;
-               }       
+                       for(SegmentationMask currentSegmentMask : segmentationMaskObjects)
+                       {
+                               currentSegmentMask.enabled = false;
+                       }
+               }
        }
        
        /**
@@ -464,6 +467,7 @@ public class SegmentationContext {
                String speciesTermName = "", collectionId = "", comment = "", curatorName = "",speciesTermId = "";
                int width = 0,height = 0;
                int noOfSegments = 0;
+               int noOfChildern = 0;
                String [][] tempStorage = null;
                SegmentationContext ctx = null;
                
@@ -472,7 +476,7 @@ public class SegmentationContext {
                        while ((entry = in.getNextEntry()) != null) {
                                String name = entry.getName();
                                
-                               if (name.equals("image.png")) {
+                               if (name.equals("image")) {
                                        imageData = SwtUtils.loadImageData(in);
                                        ctx = new SegmentationContext(imageData, file);
                                        width = imageData.width;
@@ -480,13 +484,7 @@ public class SegmentationContext {
                                }
                                
                                else if (name.startsWith("markup")) {
-                                       String[] temp;
-                                       temp = name.split("-");
-                                       int layerNumber = Integer.parseInt(temp[1].substring(0, temp[1].indexOf(".")));
                                        SegmentationMask mask = new SegmentationMask(width,height);
-                                       mask.layerNumber = layerNumber;
-                                       
-                                       
                                        InputStream input = zip.getInputStream(entry);
                                        segmentationMaskObjects.add(setMaskPixelValues(input,mask,width,height));
                                }
@@ -522,7 +520,8 @@ public class SegmentationContext {
                                        // getting collection ids
                                        NodeList nlist = docEle.getElementsByTagName("segment");
                                        noOfSegments = nlist.getLength();
-                                       tempStorage = new String[nlist.getLength()][4];
+                                       noOfChildern = nlist.item(0).getChildNodes().getLength();
+                                       tempStorage = new String[noOfSegments][noOfChildern];
                                                if(nlist != null && nlist.getLength() > 0)
                                                {
                                                        for(int i = 0 ; i < nlist.getLength();i++) 
@@ -540,7 +539,7 @@ public class SegmentationContext {
                                                                
                                                        }
                                                }
-                                       SegmentationView.speciesCombo.setText(speciesTermName);
+                                               SegmentationView.speciesCombo.setText(speciesTermName);
                                        SegmentationView.speciesCombo.setData(speciesTermName,speciesTermId);
                                        SegmentationView.curatorCombo.setText(curatorName);
                                                SegmentationView.collectionId.setText(collectionId);
@@ -551,17 +550,17 @@ public class SegmentationContext {
                                                System.out.println("XML exception"+e.toString());
                                        }
                                }
-                               
                        }
                } 
-           catch(Exception ex)
+           catch(Exception e)
            {
+               System.out.println("Exception is "+e.toString());
            }
                finally
                {
                        for(int i = 0 ; i < noOfSegments;i++) 
                        {
-                               for(int x = 0 ; x < 4;x++) 
+                               for(int x = 0 ; x < noOfChildern;x++) 
                                {
                                        if (x == 1)
                                        {

diff --git a/Annotation/src/ie/dcu/segment/SegmentationMask.java b/Annotation/src/ie/dcu/segment/SegmentationMask.java
index c9a0783eff81aa95a56c9772a2d1ee37b92a4fe0..56cb6f39be287ab01c9746d90473c86179dac685 100644 (file)
--- a/Annotation/src/ie/dcu/segment/SegmentationMask.java
+++ b/Annotation/src/ie/dcu/segment/SegmentationMask.java
@@ -67,6 +67,9 @@ public class SegmentationMask extends ByteMatrix{
        
        //The layering number of the segmentation mask.
        public int layerNumber;
+
+       //The color of the mask
+       public String maskColor;
        
        @Deprecated
        //The name(label) associated with each segment. - replaced with Term object

diff --git a/Annotation/src/ie/dcu/segment/painters/CombinedPainter.java b/Annotation/src/ie/dcu/segment/painters/CombinedPainter.java
index b9e2842ce89217a79bc2051d0d9953602124df71..9e2064a76d855a13e573afb2ae6fd83fbdadab32 100644 (file)
--- a/Annotation/src/ie/dcu/segment/painters/CombinedPainter.java
+++ b/Annotation/src/ie/dcu/segment/painters/CombinedPainter.java
@@ -106,6 +106,7 @@ public class CombinedPainter implements SegmentationPainter {
                if (isNewMaskDataRequired(mask)) {
                        mask.maskImageData = createMaskData(mask.getBounds());
                } 
+               byte main_index = 9;
                // Blit in pixels
                for (int y = 0, i = 0; y < mask.height; y++) {
                        int rowOffset = y * mask.maskImageData.bytesPerLine;
@@ -131,12 +132,13 @@ public class CombinedPainter implements SegmentationPainter {
                                // the buffer), so we can't directly copy in at the same index as the
                                // mask.
                                mask.maskImageData.data[x + rowOffset] = index;
-                               //System.out.println(mask.maskImageData.data[x + rowOffset]);
+                               
                                // However, the alpha data is always aligned correctly
                                mask.maskImageData.alphaData[i] = alpha;
                                
                                // Next location in the mask
                                i++;
+                               main_index = index;
                        }
                }
        // Create new mask
@@ -262,7 +264,7 @@ public class CombinedPainter implements SegmentationPainter {
        }
        
        public void dispose() {
-               /*// Dispose mask
+/*             // Dispose mask
                if (maskImage != null) {
                        if (!maskImage.isDisposed()) {
                                maskImage.dispose();