Support for scaling a specific region

.gitignore

@@ -4,4 +4,9 @@
 *.jar
 *.war
 *.ear
-/target
+target
+.classpath
+.project
+.settings
+*.iml
+.idea

README.md

@@ -102,20 +102,20 @@ exported in scale level 0 pixels in <em>xyz</em> orientation (long, 0)</dd>
 <dd>width of exported image tiles in pixels (int, 256)</dd>
 <dt>tileHeight</dt>
 <dd>height of exported image tiles in pixels (int, 256)</dd>
-<dt>exportMinZ</dt>
+<dt>exportedMinZ</dt>
 <dd>first <em>z</em>-section index to be exported (long, 0)</dd>
-<dt>exportMaxZ</dt>
+<dt>exportedMaxZ</dt>
 <dd>last <em>z</em>-section index to be exported (long, depth-1)</dd>
-<dt>exportMinR</dt>
-<dd>first row of tiles to be exported (long, 0)</dd>
-<dt>exportMaxR</dt>
-<dd>last row of tiles to be exported (long, depth-1)</dd>
-<dt>exportMinC</dt>
-<dd>first column of tiles to be exported (long, 0)</dd>
-<dt>exportMaxC</dt>
-<dd>last column of tiles to be exported (long, depth-1)</dd>
+<dt>exportedMinX</dt>
+<dd>first X in level 0 pixel coordinates to be exported (long, 0)</dd>
+<dt>exportedMaxX</dt>
+<dd>last X in level 0 pixel coordinates to be exported (long, width-1)</dd>
+<dt>exportedMinY</dt>
+<dd>first Y in level 0 pixel coordinates to be exported (long, 0)</dd>
+<dt>exportedMaxY</dt>
+<dd>last Y in level 0 pixel coordinates to be exported (long, depth-1)</dd>
 <dt>exportBasePath</dt>
-<dd>base path for the stakc to be exported (string, "")</dd>
+<dd>base path for the stack to be exported (string, "")</dd>
 <dt>tilePattern</dt>
 <dd>tilePattern the file name convention for export tile coordinates without
 extension and base path, must contain "&lt;s&gt;","&lt;z&gt;", "&lt;r&gt;",
@@ -155,7 +155,7 @@ contains all parameters in key=value rows (escaped according to Bash's needs).
     depth=100
     orientation=xy
     exportBasePath=/var/www/catmaid/test/xy/
-    tilePattern="<z>/<r>_<c>_<s>"
+    tilePattern="%5$d/%8$d_%9$d_%1$d.jpg"
     format=jpg
     quality=0.85
     type=gray

pom.xml

@@ -22,11 +22,17 @@
   		<artifactId>imglib2</artifactId>
   		<version>2.0.0-SNAPSHOT</version>
   	</dependency>
-  	<dependency>
+   	<dependency>
   		<groupId>net.imglib2</groupId>
   		<artifactId>imglib2-realtransform</artifactId>
   		<version>2.0.0-SNAPSHOT</version>
   	</dependency>
+   	<dependency>
+  	  <groupId>com.google.guava</groupId>
+  		<artifactId>guava</artifactId>
+  		<version>19.0</version>
+  	</dependency>
+
   </dependencies>
   <build>
     <defaultGoal>install</defaultGoal>
@@ -35,8 +41,8 @@
           <artifactId>maven-compiler-plugin</artifactId>
           <version>2.5</version>
           <configuration>
-            <source>1.6</source>
-            <target>1.6</target>
+            <source>1.7</source>
+            <target>1.7</target>
             <compilerArgument></compilerArgument>
           </configuration>
         </plugin>

src/main/java/org/catmaid/CATMAIDRandomAccessibleInterval.java

@@ -39,13 +39,15 @@
 
 import java.awt.image.BufferedImage;
 import java.awt.image.PixelGrabber;
-import java.io.IOException;
-import java.lang.ref.SoftReference;
 import java.net.URL;
-import java.util.HashMap;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutionException;
 
 import javax.imageio.ImageIO;
 
+import com.google.common.cache.Cache;
+import com.google.common.cache.CacheBuilder;
+
 import net.imglib2.AbstractInterval;
 import net.imglib2.AbstractLocalizable;
 import net.imglib2.Interval;
@@ -122,30 +124,17 @@ public int hashCode() {
 			return ( int )( value ^ ( value >>> 32 ) );
 		}
 	}
-	
+
 	class Entry
 	{
-		final protected Key key;
-		final protected int[] data;
+		final int[] data;
 
-		public Entry( final Key key, final int[] data )
+		public Entry( final int[] data )
 		{
-			this.key = key;
 			this.data = data;
 		}
-
-		@Override
-		public void finalize()
-		{
-			synchronized ( cache )
-			{
-//				System.out.println( "finalizing..." );
-				cache.remove( key );
-//				System.out.println( cache.size() + " tiles chached." );
-			}
-		}
 	}
-	
+
 	public class CATMAIDRandomAccess extends AbstractLocalizable implements RandomAccess< ARGBType >
 	{
 		protected long r, c;
@@ -590,22 +579,24 @@ public CATMAIDRandomAccess copyRandomAccess()
 			return copy();
 		}
 	}
-
-	final protected HashMap< Key, SoftReference< Entry > > cache = new HashMap< CATMAIDRandomAccessibleInterval.Key, SoftReference< Entry > >();
-	final protected String urlFormat;
-	final protected long rows, cols, s;
-	final protected int tileWidth, tileHeight;
-	final protected double scale;
-
-
+
+	private static final int MAX_CACHE_SIZE = 2048;
+
+	final private Cache< Key, Entry > tileCache;
+	final private String urlFormat;
+	final private long rows, cols, s;
+	final private int tileWidth, tileHeight;
+	final private double scale;
+
 	public CATMAIDRandomAccessibleInterval(
 			final String urlFormat,
 			final long width,
 			final long height,
 			final long depth,
 			final long s,
 			final int tileWidth,
-			final int tileHeight )
+			final int tileHeight,
+			final int cacheSize )
 	{
 		super( 3 );
 		this.urlFormat = urlFormat;
@@ -618,8 +609,12 @@ public CATMAIDRandomAccessibleInterval(
 		max[ 0 ] = ( long )( width * scale ) - 1;
 		max[ 1 ] = ( long )( height * scale ) - 1;
 		max[ 2 ] = depth - 1;
+		tileCache = CacheBuilder.newBuilder()
+						.maximumSize(cacheSize > 0 ? cacheSize : MAX_CACHE_SIZE)
+						.weakValues()
+						.build();
 	}
-	
+
 	@Override
 	public int numDimensions()
 	{
@@ -646,57 +641,46 @@ protected int[] fetchPixels( final long r, final long c, final long z )
 		}
 		catch ( final OutOfMemoryError e )
 		{
+			System.err.println("Out of memory error while fetching tile (" + c + "," + r + "," + z + "). Trying to recover");
 			System.gc();
 			return fetchPixels2( r, c, z );
 		}
 	}
 
 	protected int[] fetchPixels2( final long r, final long c, final long z )
 	{
+		Entry tileEntry = null;
 		final Key key = new Key( r, c, z );
-		synchronized ( cache )
-		{
-			final SoftReference< Entry > cachedReference = cache.get( key );
-			if ( cachedReference != null )
-			{
-				final Entry cachedEntry = cachedReference.get();
-				if ( cachedEntry != null )
-					return cachedEntry.data;
-			}
-
-			final String urlString = String.format( urlFormat, s, scale, c * tileWidth, r * tileHeight, z, tileWidth, tileHeight, r, c );
+		try {
+			tileEntry = tileCache.get(key, new Callable<Entry>() {
+				@Override
+				public Entry call() {
+					final String urlString = String.format( urlFormat, s, scale, c * tileWidth, r * tileHeight, z, tileWidth, tileHeight, r, c );
+					final int[] pixels = new int[ tileWidth * tileHeight ];
+					try {
+						System.out.println( "Load s=" + s + " r=" + r + " c=" + c + " z=" + z + " url(" + urlString + ")" );
+						final URL url = new URL( urlString );
+						final BufferedImage jpg = ImageIO.read( url );
 
-			final int[] pixels = new int[ tileWidth * tileHeight ];
-			try
-			{
-				final URL url = new URL( urlString );
-//				final Image image = toolkit.createImage( url );
-			    final BufferedImage jpg = ImageIO.read( url );
-
-				/* This gymnastic is necessary to get reproducible gray
-				 * values, just opening a JPG or PNG, even when saved by
-				 * ImageIO, and grabbing its pixels results in gray values
-				 * with a non-matching gamma transfer function, I cannot tell
-				 * why... */
-			    final BufferedImage image = new BufferedImage( tileWidth, tileHeight, BufferedImage.TYPE_INT_RGB );
-				image.createGraphics().drawImage( jpg, 0, 0, null );
-				final PixelGrabber pg = new PixelGrabber( image, 0, 0, tileWidth, tileHeight, pixels, 0, tileWidth );
-				pg.grabPixels();
-
-				cache.put( key, new SoftReference< Entry >( new Entry( key, pixels ) ) );
-//				System.out.println( "success loading r=" + r + " c=" + c + " url(" + urlString + ")" );
-
-			}
-			catch (final IOException e)
-			{
-				System.out.println( "failed loading r=" + r + " c=" + c + " url(" + urlString + ")" );
-				cache.put( key, new SoftReference< Entry >( new Entry( key, pixels ) ) );
-			}
-			catch (final InterruptedException e)
-			{
-				e.printStackTrace();
-			}
-			return pixels;
+						/* This gymnastic is necessary to get reproducible gray
+						 * values, just opening a JPG or PNG, even when saved by
+						 * ImageIO, and grabbing its pixels results in gray values
+						 * with a non-matching gamma transfer function, I cannot tell
+						 * why... */
+						final BufferedImage image = new BufferedImage( tileWidth, tileHeight, BufferedImage.TYPE_INT_RGB );
+						image.createGraphics().drawImage( jpg, 0, 0, null );
+						final PixelGrabber pg = new PixelGrabber( image, 0, 0, tileWidth, tileHeight, pixels, 0, tileWidth );
+						pg.grabPixels();
+						System.out.println( "Successfully loaded  s=" + s + " r=" + r + " c=" + c + " z=" + z + " url(" + urlString + ")" );
+					} catch (final Exception e) {
+						System.out.println( "Failed loading  s=" + s + " r=" + r + " c=" + c + " z=" + z + " url(" + urlString + ")" );
+					}
+					return new Entry(pixels);
+				}
+			});
+		} catch (ExecutionException ee) {
+			ee.printStackTrace();
 		}
+		return tileEntry != null ? tileEntry.data : null;
 	}
 }

src/main/java/org/catmaid/Downsampler.java

@@ -98,8 +98,8 @@ final static public void downsampleBytes( final byte[] aPixels, final byte[] bPi
 			}
 		}
 	}
-	
-	final static public void downsampleRGB( final int[] aPixels, final int[] bPixels, final int wa, final int ha )
+
+	final static public boolean downsampleRGB( final int[] aPixels, final int[] bPixels, final int wa, final int ha, int bgValue )
 	{
 		assert aPixels.length == wa * ha && bPixels.length == wa / 2 * ( ha / 2 ) : "Input dimensions do not match.";
 
@@ -108,15 +108,20 @@ final static public void downsampleRGB( final int[] aPixels, final int[] bPixels
 		final int wb = wa / 2;
 		final int hb = ha / 2;
 		final int nb = hb * wb;
-
+		boolean bresult = false;
 		for ( int ya = 0, yb = 0; yb < nb; ya += wa2, yb += wb )
 		{
 			final int ya1 = ya + wa;
 			for ( int xa = 0, xb = 0; xb < wb; xa += 2, ++xb )
 			{
 				final int xa1 = xa + 1;
-				bPixels[ yb + xb ] = averageColor( ya + xa, ya + xa1, ya1 + xa, ya1 + xa1, aPixels );
+				int c = averageColor( ya + xa, ya + xa1, ya1 + xa, ya1 + xa1, aPixels );
+				bPixels[ yb + xb ] = c;
+				if ((c & 0xFFFFFF) != bgValue) {
+					bresult = true; // return true since at least one pixel is non black
+				}
 			}
 		}
+		return bresult;
 	}
 }