Merge pull request ome#5761 from dominikl/shapedata_bugfix

Shapedata bugfix
melissalinkert · Jul 6, 2018 · 69e49a7 · 69e49a7
2 parents d61e7b8 + a0f1bd0
commit 69e49a7
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Showing 15 changed files with 563 additions and 67 deletions.
diff --git a/components/blitz/src/omero/gateway/facility/ROIFacility.java b/components/blitz/src/omero/gateway/facility/ROIFacility.java
@@ -702,8 +702,8 @@ public Collection<ROIData> saveROIs(SecurityContext ctx, long imageID,
                         for (int i = 0 ; i < serverRoi.sizeOfShapes(); i++) {
                             s = serverRoi.getShape(i);
                             if (s != null) {
-                                z = 0;
-                                t = 0;
+                                z = -1;
+                                t = -1;
                                 if (s.getTheZ() != null) z = s.getTheZ().getValue();
                                 if (s.getTheT() != null) t = s.getTheT().getValue();
                                 serverCoordMap.put(new ROICoordinate(z, t), s);

diff --git a/components/blitz/src/omero/gateway/model/LineData.java b/components/blitz/src/omero/gateway/model/LineData.java
@@ -100,6 +100,7 @@ public void setText(String text)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setTextValue(rtypes.rstring(text));
+        setDirty(true);
     }
 
     /**
@@ -128,6 +129,7 @@ public void setX1(double x1)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setX1(rtypes.rdouble(x1));
+        setDirty(true);
     }
 
     /**
@@ -156,6 +158,7 @@ public void setX2(double x2)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setX2(rtypes.rdouble(x2));
+        setDirty(true);
     }
 
     /**
@@ -184,6 +187,7 @@ public void setY1(double y1)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setY1(rtypes.rdouble(y1));
+        setDirty(true);
     }
 
     /**
@@ -212,6 +216,7 @@ public void setY2(double y2)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setY2(rtypes.rdouble(y2));
+        setDirty(true);
     }
 
 }
diff --git a/components/blitz/src/omero/gateway/model/MaskData.java b/components/blitz/src/omero/gateway/model/MaskData.java
@@ -107,6 +107,7 @@ public void setText(String text)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setTextValue(rtypes.rstring(text));
+        setDirty(true);
     }
 
     /**
@@ -135,6 +136,7 @@ public void setX(double x)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setX(rtypes.rdouble(x));
+        setDirty(true);
     }
 
     /**
@@ -163,6 +165,7 @@ public void setY(double y)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setY(rtypes.rdouble(y));
+        setDirty(true);
     }
 
     /**
@@ -191,6 +194,7 @@ public void setWidth(double width)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setWidth(rtypes.rdouble(width));
+        setDirty(true);
     }
 
     /**
@@ -219,6 +223,7 @@ public void setHeight(double height)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setHeight(rtypes.rdouble(height));
+        setDirty(true);
     }
 
     /**
@@ -230,6 +235,7 @@ public void setMask(byte[] mask)
     {
         Mask shape = (Mask) asIObject();
         shape.setBytes(mask);	
+        setDirty(true);
     }
 
     /**
@@ -255,6 +261,7 @@ public void setMask(BufferedImage image)
                     }
                     setBit(data, (int)(y*getWidth()+x), 1);
                 }
+        setDirty(true);
     }
 
     /**
@@ -343,6 +350,7 @@ public void setBit(byte[] data, int bit, int val)
         data[bytePosition] = (byte) ((byte)(data[bytePosition]&
                 (~(byte)(0x1<<bitPosition)))|
                 (byte)(val<<bitPosition));
+        setDirty(true);
     }
 
     /** 

diff --git a/components/blitz/src/omero/gateway/model/PointData.java b/components/blitz/src/omero/gateway/model/PointData.java
@@ -100,6 +100,7 @@ public void setText(String text)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setTextValue(rtypes.rstring(text));
+        setDirty(true);
     }
 
 
@@ -130,6 +131,7 @@ public void setX(double x)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setX(rtypes.rdouble(x));
+        setDirty(true);
     }
 
     /**
@@ -159,6 +161,7 @@ public void setY(double y)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setY(rtypes.rdouble(y));
+        setDirty(true);
     }
 
 }
diff --git a/components/blitz/src/omero/gateway/model/PolygonData.java b/components/blitz/src/omero/gateway/model/PolygonData.java
@@ -97,6 +97,7 @@ public void setText(String text)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setTextValue(rtypes.rstring(text));
+        setDirty(true);
     }
 
     /**
@@ -138,6 +139,7 @@ public void setPoints(List<Point2D.Double> points)
         String pointsValues =
                 toPoints(points.toArray(new Point2D.Double[points.size()]));
         shape.setPoints(rtypes.rstring(pointsValues));
+        setDirty(true);
     }
 
 }
diff --git a/components/blitz/src/omero/gateway/model/PolylineData.java b/components/blitz/src/omero/gateway/model/PolylineData.java
@@ -100,6 +100,7 @@ public void setText(String text)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setTextValue(rtypes.rstring(text));
+        setDirty(true);
     }
 
     /**
@@ -129,5 +130,6 @@ public void setPoints(List<Point2D.Double> points)
         String pointsValues =
                 toPoints(points.toArray(new Point2D.Double[points.size()]));
         shape.setPoints(rtypes.rstring(pointsValues));
+        setDirty(true);
     }
 }
diff --git a/components/blitz/src/omero/gateway/model/ROICoordinate.java b/components/blitz/src/omero/gateway/model/ROICoordinate.java
@@ -1,6 +1,6 @@
 /*
  *------------------------------------------------------------------------------
- * Copyright (C) 2006-2009 University of Dundee. All rights reserved.
+ * Copyright (C) 2006-2018 University of Dundee. All rights reserved.
  *
  *
  * This program is free software; you can redistribute it and/or modify
@@ -58,8 +58,8 @@ public ROICoordinate()
     /**
      * Creates a new instance.
      *
-     * @param z The z-section.
-     * @param t The timepoint.
+     * @param z The z-section. (-1 == all z-sections)
+     * @param t The timepoint. (-1 == all timepoints)
      */
     public ROICoordinate(int z, int t)
     {
@@ -69,22 +69,21 @@ public ROICoordinate(int z, int t)
 
     /**
      * Returns the timepoint.
-     *
+     * (-1 == all timepoints)
      * @return See above.
      */
     public int getTimePoint() { return t; }
 
     /**
      * Returns the z-section.
-     *
+     * (-1 == all z-sections)
      * @return See above.
      */
     public int getZSection() { return z; }
 
     /**
      * Implemented as specified by the {@link Comparator} I/F.
      * @see Comparator#compare(Object, Object)
-     * If any attribute == -1 it is not included in comparison.
      */
     public int compare(Object o1, Object o2)
     {
@@ -101,7 +100,6 @@ public int compare(Object o1, Object o2)
 
     /**
      * Overridden to control if the passed object equals the current one.
-     * If any attribute == -1 it is not included in comparison.
      * @see java.lang.Object#equals(Object)
      */
     public boolean equals(Object obj)

diff --git a/components/blitz/src/omero/gateway/model/ROIData.java b/components/blitz/src/omero/gateway/model/ROIData.java
@@ -1,6 +1,6 @@
 /*
  *------------------------------------------------------------------------------
- * Copyright (C) 2006-2016 University of Dundee. All rights reserved.
+ * Copyright (C) 2006-2018 University of Dundee. All rights reserved.
  *
  *
  * This program is free software; you can redistribute it and/or modify
@@ -207,17 +207,21 @@ public void removeShapeData(ShapeData shape)
         if (roi == null) 
             throw new IllegalArgumentException("No Roi specified.");
         ROICoordinate coord = shape.getROICoordinate();
-        List<ShapeData> shapeList;
-        shapeList = roiShapes.get(coord);
-        shapeList.remove(shape);
-        roi.removeShape((Shape) shape.asIObject());
-        setDirty(true);
+        List<ShapeData> shapeList = roiShapes.get(coord);
+        if (shapeList != null) {
+            shapeList.remove(shape);
+            roi.removeShape((Shape) shape.asIObject());
+            setDirty(true);
+        }
     }
 
     /**
      * Returns the number of planes occupied by the ROI.
      *
      * @return See above.
+     * @deprecated Will be removed in future. Does not work as 
+     * expected if the ROI contains shapes which are associated 
+     * with all planes (Z, C, T == -1)
      */
     public int getPlaneCount() { return roiShapes.size(); }
 
@@ -247,7 +251,19 @@ public int getShapeCount()
      */
     public List<ShapeData> getShapes(int z, int t)
     {
-        return roiShapes.get(new ROICoordinate(z, t));
+        List<ShapeData> res = roiShapes.get(new ROICoordinate(z, t));
+        if (res == null)
+            res = new ArrayList<ShapeData>();
+        List<ShapeData> allZT = roiShapes.get(new ROICoordinate(-1, -1));
+        if (allZT != null)
+            res.addAll(allZT);
+        List<ShapeData> allZ = roiShapes.get(new ROICoordinate(-1, t));
+        if (allZ != null)
+            res.addAll(allZ);
+        List<ShapeData> allT = roiShapes.get(new ROICoordinate(z, -1));
+        if (allT != null)
+            res.addAll(allT);
+        return res;
     }
 
     /**
@@ -260,38 +276,53 @@ public Iterator<List<ShapeData>> getIterator()
         return roiShapes.values().iterator();
     }
 
-    /** 
+    /**
      * Return the first plane that the ROI starts on.
      *
      * @return See above.
+     * @deprecated Will be removed in future. Does not work as 
+     * expected if the ROI contains shapes which are associated 
+     * with all planes (Z, C, T == -1)
      */
-    public ROICoordinate firstPlane()
-    {
+    public ROICoordinate firstPlane() {
         return roiShapes.firstKey();
     }
 
-    /** 
+    /**
      * Returns the last plane that the ROI ends on.
      *
      * @return See above.
+     * @deprecated Will be removed in future. Does not work as 
+     * expected if the ROI contains shapes which are associated 
+     * with all planes (Z, C, T == -1)
      */
-    public ROICoordinate lastPlane()
-    {
+    public ROICoordinate lastPlane() {
         return roiShapes.lastKey();
     }
 
     /**
      * Returns an iterator of the Shapes in the ROI in the range [start, end].
      *
-     * @param start The starting plane where the Shapes should reside.
-     * @param end The final plane where the Shapes should reside.
+     * @param start
+     *            The starting plane where the Shapes should reside.
+     * @param end
+     *            The final plane where the Shapes should reside.
      * @return See above.
+     * @deprecated Will be removed in future. Does not work as
+     * expected if the ROI contains shapes which are associated
+     * with all planes (Z, C, T == -1)
      */
     public Iterator<List<ShapeData>> getShapesInRange(ROICoordinate start,
-            ROICoordinate end)
-            {
-        return roiShapes.subMap(start, end).values().iterator();
-            }
+            ROICoordinate end) {
+        List<List<ShapeData>> res = new ArrayList<List<ShapeData>>();
+        Collection<List<ShapeData>> inRange = roiShapes.subMap(start, end).values();
+        if (inRange != null)
+            res.addAll(inRange);
+        List<ShapeData> allRanges = roiShapes.get(new ROICoordinate(-1, -1));
+        if (allRanges != null)
+            res.add(allRanges);
+        return res.iterator();
+    }
 
     /**
      * Returns <code>true</code> if the object a client-side object,

diff --git a/components/blitz/src/omero/gateway/model/RectangleData.java b/components/blitz/src/omero/gateway/model/RectangleData.java
@@ -100,6 +100,7 @@ public void setText(String text)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setTextValue(rtypes.rstring(text));
+        setDirty(true);
     }
 
     /**
@@ -130,6 +131,7 @@ public void setX(double x)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setX(rtypes.rdouble(x));
+        setDirty(true);
     }
 
     /**
@@ -160,6 +162,7 @@ public void setY(double y)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setY(rtypes.rdouble(y));
+        setDirty(true);
     }
 
     /**
@@ -188,6 +191,7 @@ public void setWidth(double width)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setWidth(rtypes.rdouble(width));
+        setDirty(true);
     }
 
     /**
@@ -216,6 +220,7 @@ public void setHeight(double height)
         if (shape == null) 
             throw new IllegalArgumentException("No shape specified.");
         shape.setHeight(rtypes.rdouble(height));
+        setDirty(true);
     }
 
 }