Changeset 2588

Timestamp:

07/03/08 09:20:35 (5 months ago)

Author:

callan

Message:

Initial projection and in memory pixel buffer support (#11):

• MappedByteBuffer? --> ByteBuffer? throughout
  
• PixelData? is now read-write
  
• Eclipse .classpath fixes for common, server, rendering and client
  
• Removal of public ICompress interface
  
• IProjection added, naively assumes all projections are maximum intensity
  
• renderAsPackedInt() can now take an arbitrary pixel buffer for rendering
  
• RenderingEngine now performs projections and renders the resulting plane for display
  
• Various unused imports removed
  
• Some Javadoc cleanups
  
• Missing Blitz mappings will be added with interface cleanups
  

Location:

trunk/components

Files:

• client/.classpath (modified) (4 diffs)
• common/.classpath (modified) (2 diffs)
• common/src/ome/api/ICompress.java (deleted)
• common/src/ome/api/IProjection.java (added)
• common/src/omeis/providers/re/RenderingEngine.java (modified) (3 diffs)
• rendering/.classpath (modified) (2 diffs)
• rendering/src/omeis/providers/re/HSBStrategy.java (modified) (2 diffs)
• rendering/src/omeis/providers/re/Renderer.java (modified) (4 diffs)
• rendering/src/omeis/providers/re/RenderingStrategy.java (modified) (1 diff)
• romio/.classpath (modified) (2 diffs)
• romio/src/ome/io/nio/DeltaVision.java (modified) (8 diffs)
• romio/src/ome/io/nio/DeltaVisionHeader.java (modified) (3 diffs)
• romio/src/ome/io/nio/InMemoryPlanarPixelBuffer.java (added)
• romio/src/ome/io/nio/PixelData.java (modified) (5 diffs)
• romio/src/ome/io/nio/ReorderedPixelData.java (modified) (3 diffs)
• romio/src/ome/io/nio/RomioPixelBuffer.java (modified) (8 diffs)
• romio/test/ome/io/nio/utests/DeltaVisionTest.java (modified) (2 diffs)
• romio/test/ome/io/nio/utests/deltavision/BasicIOUnitTest.java (modified) (3 diffs)
• romio/test/ome/io/nio/utests/deltavision/DeltaVisionWZTUnitTest.java (modified) (5 diffs)
• romio/test/ome/io/nio/utests/deltavision/DeltaVisionZTWUnitTest.java (modified) (5 diffs)
• romio/test/ome/io/nio/utests/deltavision/DeltaVisionZWTUnitTest.java (modified) (5 diffs)
• romio/test/ome/io/nio/utests/deltavision/EightBitBasicIOUnitTest.java (modified) (3 diffs)
• romio/test/ome/io/nio/utests/deltavision/UnsignedSixteenBitBasicIOUnitTest.java (modified) (3 diffs)
• server/.classpath (modified) (2 diffs)
• server/resources/ome/services/service-ome.api.IProjection.xml (added)
• server/resources/ome/services/service-omeis.providers.re.RenderingEngine.xml (modified) (1 diff)
• server/src/ome/api/local/LocalCompress.java (modified) (1 diff)
• server/src/ome/logic/AWTScaleService.java (modified) (2 diffs)
• server/src/ome/logic/CompressImpl.java (modified) (1 diff)
• server/src/ome/logic/PixelsImpl.java (modified) (1 diff)
• server/src/ome/logic/RenderingSettingsImpl.java (modified) (4 diffs)
• server/src/ome/services/RawPixelsBean.java (modified) (2 diffs)
• server/src/ome/services/RenderingBean.java (modified) (11 diffs)
• server/src/ome/services/ThumbnailBean.java (modified) (1 diff)
• server/src/ome/services/projection (added)
• server/src/ome/services/projection/ProjectionBean.java (added)

trunk/components/client/.classpath

@@ -9 +9 @@
         <classpathentry kind="lib" path="target/libs/ant.jar"/>
         <classpathentry kind="lib" path="target/libs/antlr.jar"/>
-        <classpathentry kind="lib" path="target/libs/asm.jar"/>
-        <classpathentry kind="lib" path="target/libs/asm-attrs.jar"/>
-        <classpathentry kind="lib" path="target/libs/cglib.jar"/>
         <classpathentry kind="lib" path="target/libs/checkstyle.jar"/>
         <classpathentry kind="lib" path="target/libs/common.jar"/>
@@ -17 +14 @@
         <classpathentry kind="lib" path="target/libs/commons-collections.jar"/>
         <classpathentry kind="lib" path="target/libs/commons-logging.jar"/>
-        <classpathentry kind="lib" path="target/libs/dom4j.jar"/>
         <classpathentry kind="lib" path="target/libs/dsl.jar"/>
-        <classpathentry kind="lib" path="target/libs/ehcache.jar"/>
         <classpathentry kind="lib" path="target/libs/emma_ant.jar"/>
         <classpathentry kind="lib" path="target/libs/emma.jar"/>
@@ -25 +20 @@
         <classpathentry kind="lib" path="target/libs/freemarker.jar"/>
         <classpathentry kind="lib" path="target/libs/groovy.jar"/>
-        <classpathentry kind="lib" path="target/libs/hibernate.jar"/>
         <classpathentry kind="lib" path="target/libs/hibernate-annotations.jar"/>
         <classpathentry kind="lib" path="target/libs/hibernate-commons-annotations.jar"/>
@@ -43 +37 @@
         <classpathentry kind="lib" path="target/libs/persistence-api.jar"/>
         <classpathentry kind="lib" path="target/libs/postgresql.jar"/>
-        <classpathentry kind="lib" path="target/libs/qdox.jar"/>
         <classpathentry kind="lib" path="target/libs/spring.jar"/>
         <classpathentry kind="lib" path="target/libs/spring-mock.jar"/>

trunk/components/common/.classpath

@@ -18 +18 @@
         <classpathentry kind="lib" path="target/libs/dom4j.jar"/>
         <classpathentry kind="lib" path="target/libs/dsl.jar"/>
-        <classpathentry kind="lib" path="target/libs/ehcache.jar"/>
         <classpathentry kind="lib" path="target/libs/emma_ant.jar"/>
         <classpathentry kind="lib" path="target/libs/emma.jar"/>
@@ -41 +40 @@
         <classpathentry kind="lib" path="target/libs/persistence-api.jar"/>
         <classpathentry kind="lib" path="target/libs/postgresql.jar"/>
-        <classpathentry kind="lib" path="target/libs/qdox.jar"/>
         <classpathentry kind="lib" path="target/libs/spring.jar"/>
         <classpathentry kind="lib" path="target/libs/spring-mock.jar"/>

trunk/components/common/src/omeis/providers/re/RenderingEngine.java

@@ -78 +78 @@
      *             If <code>pd</code> is <code>null</code>.
      */
-    public RGBBuffer render(PlaneDef pd) throws ValidationException;
+    public RGBBuffer render(PlaneDef pd);
 
     /**
@@ -95 +95 @@
      * @see render()
      */
-    public int[] renderAsPackedInt(PlaneDef pd) throws ValidationException;
+    public int[] renderAsPackedInt(PlaneDef pd);
     
     /**
@@ -110 +110 @@
      * @see renderAsPackedInt()
      */
-    public byte[] renderCompressed(PlaneDef pd) throws ValidationException;
+    public byte[] renderCompressed(PlaneDef pd);
+    
+    
+    /**
+     * Performs a projection through selected optical sections of a particular 
+     * timepoint with the currently active channels and renders the data for
+     * display.
+     * @param algorithm {@link IProjection#MAXIMUM_INTENSITY},
+     * {@link IProjection#MEAN_INTENSITY} or {@link IProjection#SUM_INTENSITY}.
+     * @param stepping Stepping value to use while calculating the projection.
+     * For example, <code>stepping=1</code> will use every optical section from
+     * <code>start</code> to <code>end</code> where <code>stepping=2</code> will
+     * use every other section from <code>start</code> to <code>end</code> to
+     * perform the projection.
+     * @param start Optical section to start projecting from.
+     * @param end Optical section to finish projecting.
+     * @return A packed-integer <i>RGBA</i> rendered image of the projected
+     * pixels.
+     * @throws ValidationException Where:
+     * <ul>
+     *   <li><code>algorithm</code> is unknown</li>
+     *   <li><code>timepoint</code> is out of range</li>
+     *   <li><code>start</code> is out of range</li>
+     *   <li><code>end</code> is out of range</li>
+     *   <li><code>start > end</code></li>
+     * </ul>
+     * @see IPixels#projectPixels()
+     */
+    public int[] renderProjectedAsPackedInt(int algorithm, int timepoint,
+                                            int stepping, int start, int end);
+    
+    /**
+     * Performs a projection through selected optical sections of a particular 
+     * timepoint with the currently active channels, renders the data for
+     * display and compresses the resulting RGBA composite image.
+     * @param algorithm {@link IProjection#MAXIMUM_INTENSITY},
+     * {@link IProjection#MEAN_INTENSITY} or {@link IProjection#SUM_INTENSITY}.
+     * @param stepping Stepping value to use while calculating the projection.
+     * For example, <code>stepping=1</code> will use every optical section from
+     * <code>start</code> to <code>end</code> where <code>stepping=2</code> will
+     * use every other section from <code>start</code> to <code>end</code> to
+     * perform the projection.
+     * @param start Optical section to start projecting from.
+     * @param end Optical section to finish projecting.
+     * @return A compressed <i>RGBA</i> rendered JPEG image of the projected
+     * pixels.
+     * @throws ValidationException Where:
+     * <ul>
+     *   <li><code>algorithm</code> is unknown</li>
+     *   <li><code>timepoint</code> is out of range</li>
+     *   <li><code>start</code> is out of range</li>
+     *   <li><code>end</code> is out of range</li>
+     *   <li><code>start > end</code></li>
+     * </ul>
+     * @see IPixels#projectPixels()
+     */
+    public byte[] renderProjectedCompressed(int algorithm, int timepoint,
+                                            int stepping, int start, int end);
 
     /**

trunk/components/rendering/.classpath

@@ -19 +19 @@
         <classpathentry kind="lib" path="target/libs/dom4j.jar"/>
         <classpathentry kind="lib" path="target/libs/dsl.jar"/>
-        <classpathentry kind="lib" path="target/libs/ehcache.jar"/>
         <classpathentry kind="lib" path="target/libs/emma_ant.jar"/>
         <classpathentry kind="lib" path="target/libs/emma.jar"/>
@@ -42 +41 @@
         <classpathentry kind="lib" path="target/libs/persistence-api.jar"/>
         <classpathentry kind="lib" path="target/libs/postgresql.jar"/>
-        <classpathentry kind="lib" path="target/libs/qdox.jar"/>
         <classpathentry kind="lib" path="target/libs/romio.jar"/>
         <classpathentry kind="lib" path="target/libs/spring.jar"/>

trunk/components/rendering/src/omeis/providers/re/HSBStrategy.java

@@ -42 +42 @@
  * Transforms a plane within a given pixels set into an <i>RGB</i> image. As
  * many wavelengths (channels) as desired can contribute to the final image and
- * each wavelength is mapped to a color. All this things are specified by the
+ * each wavelength is mapped to a color. All these things are specified by the
  * rendering context.
  * <p>
- * When multiple wavelengths have to be combined into the final image (this is
- * the case if the rendering context specifies more than one active channel),
- * this strategy renders each wavelength in a separate thread &#151; this often
- * results in parallel rendering on multi-processor machines.
+ * This strategy renders the in "regions", dividing the planar data up based
+ * on {@link #maxTasks} and assigning each task to its own thread. This should
+ * result in parallel rendering on multi-processor machines.
  * </p>
  * <p>
  * Thread-safety relies on the fact that the rendering context is not going to
- * change during the whole image rendering process. (This is enforced by the
- * {@link RenderingEngineImpl}; in fact, while the <code>render</code> method
- * executes, the whole component is locked.)
+ * change during the whole image rendering process and that each task is
+ * working on its own atomic unit of work.
  * </p>
  * 
@@ -261 +259 @@
      * Implemented as specified by the superclass.
      * 
-     * @see RenderingStrategy#render(Renderer ctx, PlaneDef planeDef)
+     * @see RenderingStrategy#renderAsPackedInt(Renderer ctx, PlaneDef planeDef)
      */
     @Override

trunk/components/rendering/src/omeis/providers/re/Renderer.java

@@ -20 +20 @@
 // Application-internal dependencies
 import ome.conditions.ResourceError;
+import ome.conditions.ValidationException;
 import ome.io.nio.PixelBuffer;
 import ome.model.core.Channel;
@@ -422 +423 @@
      *            Selects a plane orthogonal to one of the <i>X</i>, <i>Y</i>,
      *            or <i>Z</i> axes.
+     * @param newBuffer
+     *             The pixel buffer to use in place of the one currently
+     *             defined in the renderer. This will not change the state
+     *             of the Renderer. If <code>null</code> is passed the existing
+     *             pixel buffer will be used.
      * @return An <i>RGB</i> image ready to be displayed on screen.
      * @throws IOException
-     *             If an error occured while trying to pull out data from the
+     *             If an error occurred while trying to pull out data from the
      *             pixels data repository.
      * @throws QuantizationException
@@ -431 +437 @@
      *             If <code>pd</code> is <code>null</code>.
      */
-    public int[] renderAsPackedInt(PlaneDef pd) throws IOException,
-            QuantizationException {
+    public int[] renderAsPackedInt(PlaneDef pd, PixelBuffer newBuffer)
+        throws IOException, QuantizationException
+    {
         if (pd == null) {
             throw new NullPointerException("No plane definition.");
@@ -439 +446 @@
         log.info("Using: '" + renderingStrategy.getClass().getName()
                 + "' rendering strategy.");
-        RGBIntBuffer img = renderingStrategy.renderAsPackedInt(this, pd);
-        stats.stop();
-        // TODO: Commenting this out for now. -- callan
-        //log.info(stats.getStats());
-        return img.getDataBuffer();
-    }
-
+        PixelBuffer oldBuffer = buffer;
+        try
+        {
+            if (newBuffer != null)
+            {
+                buffer = newBuffer;
+            }
+            RGBIntBuffer img = renderingStrategy.renderAsPackedInt(this, pd);
+            stats.stop();
+            // TODO: Commenting this out for now. -- callan
+            //log.info(stats.getStats());
+            return img.getDataBuffer();
+        }
+        finally
+        {
+            buffer = oldBuffer;
+        }
+    }
+    
     /**
      * Returns the size, in bytes, of the {@link RGBBuffer} that would be

trunk/components/rendering/src/omeis/providers/re/RenderingStrategy.java

@@ -124 +124 @@
      * Encapsulates a specific rendering algorithm. The image is rendered
      * according to the current settings hold by the <code>ctx</code>
-     * argument. Typically, active wavelenghts are processed by first quantizing
-     * the wavelenght data in the plane selected by <code>pd</code> &#151; the
+     * argument. Typically, active wavelengths are processed by first quantizing
+     * the wavelength data in the plane selected by <code>pd</code> &#151; the
      * quantum strategy is retrieved from the {@link QuantumManager} (accessed
      * through the <code>ctx</code> object) and the actual data from the

trunk/components/romio/.classpath

@@ -19 +19 @@
         <classpathentry kind="lib" path="target/libs/dom4j.jar"/>
         <classpathentry kind="lib" path="target/libs/dsl.jar"/>
-        <classpathentry kind="lib" path="target/libs/ehcache.jar"/>
         <classpathentry kind="lib" path="target/libs/emma_ant.jar"/>
         <classpathentry kind="lib" path="target/libs/emma.jar"/>
@@ -42 +41 @@
         <classpathentry kind="lib" path="target/libs/persistence-api.jar"/>
         <classpathentry kind="lib" path="target/libs/postgresql.jar"/>
-        <classpathentry kind="lib" path="target/libs/qdox.jar"/>
         <classpathentry kind="lib" path="target/libs/spring.jar"/>
         <classpathentry kind="lib" path="target/libs/spring-mock.jar"/>

trunk/components/romio/src/ome/io/nio/DeltaVision.java

@@ -11 +11 @@
 import java.io.IOException;
 import java.io.RandomAccessFile;
-import java.nio.Buffer;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.nio.IntBuffer;
-import java.nio.MappedByteBuffer;
 import java.nio.ShortBuffer;
 import java.nio.channels.FileChannel;
@@ -52 +50 @@
         private Integer totalSize;
         
-        protected MappedByteBuffer buf;
+        protected ByteBuffer buf;
 
         private OriginalFile originalFile;
@@ -94 +92 @@
                 for (int t = 0; t < getSizeT(); t++) {
                         try {
-                                MappedByteBuffer buffer = getTimepoint(t).getData();
+                                ByteBuffer buffer = getTimepoint(t).getData();
                                 md.update(buffer);
                         } catch (DimensionsOutOfBoundsException e) {
@@ -132 +130 @@
                 if (buffer.length != count * header.getBytesPerPixel())
                         throw new ApiUsageException("Buffer size incorrect.");
-                MappedByteBuffer plane = getPlane(z, c, t).getData();
+                ByteBuffer plane = getPlane(z, c, t).getData();
                 swapAndReorderIfRequired(plane, ByteBuffer.wrap(buffer), offset, count);
                 return buffer;
@@ -157 +155 @@
                 if (buffer.length != getPlaneSize())
                         throw new ApiUsageException("Buffer size incorrect.");
-                MappedByteBuffer b = getPlane(z, c, t).getData();
+                ByteBuffer b = getPlane(z, c, t).getData();
                 swapAndReorderIfRequired(b, ByteBuffer.wrap(buffer), 
                                          0, getSizeX() * getSizeY());
@@ -192 +190 @@
                         throws IOException {
                 FileChannel fileChannel = getFileChannel();
-                MappedByteBuffer buf = fileChannel.map(MapMode.READ_ONLY, offset, size);
+                ByteBuffer buf = fileChannel.map(MapMode.READ_ONLY, offset, size);
                 if (!header.isNative())
                         buf.order(ByteOrder.LITTLE_ENDIAN);
@@ -206 +204 @@
                 if (buffer.length != size)
                         throw new ApiUsageException("Buffer size incorrect.");
-                MappedByteBuffer b = getRegion(size, offset).getData();
+                ByteBuffer b = getRegion(size, offset).getData();
                 b.get(buffer);
                 return buffer;
@@ -230 +228 @@
                 if (buffer.length != getRowSize())
                         throw new ApiUsageException("Buffer size incorrect.");
-                MappedByteBuffer b = getRow(y, z, c, t).getData();
+                ByteBuffer b = getRow(y, z, c, t).getData();
                 swapAndReorderIfRequired(b, ByteBuffer.wrap(buffer), 0, getSizeX());
                 return buffer;

trunk/components/romio/src/ome/io/nio/DeltaVisionHeader.java

@@ -1 +1 @@
 package ome.io.nio;
 
+import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.nio.MappedByteBuffer;
@@ -21 +22 @@
 public class DeltaVisionHeader {
 
-        private MappedByteBuffer data;
+        private ByteBuffer data;
         
         /**
@@ -105 +106 @@
          * @param endian
          */
-        public DeltaVisionHeader(MappedByteBuffer data, boolean endian) {
+        public DeltaVisionHeader(ByteBuffer data, boolean endian) {
                 this.data = data;
                 

trunk/components/romio/src/ome/io/nio/PixelData.java

@@ -9 +9 @@
 
 import java.nio.ByteOrder;
-import java.nio.MappedByteBuffer;
+import java.nio.ByteBuffer;
 
 import ome.model.enums.PixelsType;
@@ -46 +46 @@
     
     /** The pixels data backing buffer. */
-    protected MappedByteBuffer data;
+    protected ByteBuffer data;
     
     /** If the data is signed. */
@@ -63 +63 @@
          * @param data The raw pixel data.
          */
-        public PixelData(PixelsType pixelsType, MappedByteBuffer data)
+        public PixelData(PixelsType pixelsType, ByteBuffer data)
         {
                 this.data = data;
@@ -150 +150 @@
             return true;
         return false;
+    }
+    
+    /**
+     * Sets the pixel intensity value of the pixel at a given offset within
+     * the backing buffer. This method takes into account bytes per pixel. 
+     * 
+     * @param offset The relative offset (taking into account the number of 
+     * bytes per pixel) within the backing buffer.
+     * @param value Pixel value to set.
+     */
+    public void setPixelValue(int offset, double value)
+    {
+        setPixelValueDirect(offset * bytesPerPixel, value);
+    }
+    
+    /**
+     * Sets the pixel intensity value of the pixel at a given offset within
+     * the backing buffer. This method does not take into account bytes per
+     * pixel.
+     * 
+     * @param offset The absolute offset within the backing buffer.
+     * @param value Pixel value to set.
+     */
+    public void setPixelValueDirect(int offset, double value)
+    {
+        switch (javaType)
+        {
+            case BYTE:
+                data.put(offset, (byte) value);
+                break;
+            case SHORT:
+                data.putShort(offset, (short) value);
+                break;
+            case INT:
+                data.putInt(offset, (int) value);
+                break;
+            case FLOAT:
+                data.putFloat(offset, (float) value);
+                break;
+            case DOUBLE:
+                data.putDouble(offset, value);
+                break;
+        }
     }
     
@@ -212 +255 @@
      * @return See above.
      */
-    public MappedByteBuffer getData()
+    public ByteBuffer getData()
     {
         return data;

trunk/components/romio/src/ome/io/nio/ReorderedPixelData.java

@@ -9 +9 @@
 
 import java.nio.ByteOrder;
-import java.nio.MappedByteBuffer;
+import java.nio.ByteBuffer;
 
 import ome.conditions.ApiUsageException;
@@ -38 +38 @@
          * @param rowSize The size of each pixels row in bytes.
          */
-        public ReorderedPixelData(PixelsType pixelsType, MappedByteBuffer data,
+        public ReorderedPixelData(PixelsType pixelsType, ByteBuffer data,
                                           int rowSize)
         {
@@ -82 +82 @@
      * @return See above.
      */
-    public MappedByteBuffer getData()
+    public ByteBuffer getData()
     {
         return data;

trunk/components/romio/src/ome/io/nio/RomioPixelBuffer.java

@@ -210 +210 @@
                 if (buffer.length != size)
                         throw new ApiUsageException("Buffer size incorrect.");
-                MappedByteBuffer b = getRegion(size, offset).getData();
+                ByteBuffer b = getRegion(size, offset).getData();
                 b.get(buffer);
                 return buffer;
@@ -228 +228 @@
                 if (buffer.length != getRowSize())
                         throw new ApiUsageException("Buffer size incorrect.");
-                MappedByteBuffer b = getRow(y, z, c, t).getData();
+                ByteBuffer b = getRow(y, z, c, t).getData();
                 b.get(buffer);
                 return buffer;