Merge pull request #191 from scifio/available-memory

Fix the estimation of the remaining free memory

scifio/src/main/java/io/scif/filters/PlaneSeparator.java

@@ -39,6 +39,7 @@
 import io.scif.io.RandomAccessInputStream;
 import io.scif.util.FormatTools;
 import io.scif.util.ImageTools;
+import io.scif.util.MemoryTools;
 
 import java.io.File;
 import java.io.IOException;
@@ -262,8 +263,7 @@ public Plane openPlane(final int imageIndex, final long planeIndex,
 					// available memory, we will need to split it into strips (of the last
 					// planar axis)
 
-					final Runtime rt = Runtime.getRuntime();
-					final long availableMemory = rt.freeMemory();
+					final long availableMemory = MemoryTools.totalAvailableMemory() / 16;
 					final long planeSize = meta.get(imageIndex).getPlaneSize();
 					// If we make strips, they will be of the Y axis
 					final long h = lengths[meta.get(imageIndex).getAxisIndex(Axes.Y)];

scifio/src/main/java/io/scif/img/DefaultImgFactoryHeuristic.java

@@ -35,6 +35,7 @@
 import io.scif.config.SCIFIOConfig.ImgMode;
 import io.scif.img.cell.SCIFIOCellImgFactory;
 import io.scif.util.FormatTools;
+import io.scif.util.MemoryTools;
 import net.imglib2.exception.IncompatibleTypeException;
 import net.imglib2.img.ImgFactory;
 import net.imglib2.img.array.ArrayImgFactory;
@@ -81,7 +82,7 @@ public <T extends NativeType<T>> ImgFactory<T> createFactory(
 		final long maxSize = DataTools.safeMultiply64(2, 1024, 1024, 1024);
 
 		final long availableMem =
-			(long) (Runtime.getRuntime().freeMemory() * MEMORY_THRESHOLD);
+			(long) (MemoryTools.totalAvailableMemory() * MEMORY_THRESHOLD);
 		long datasetSize = m.getDatasetSize();
 
 		// check for overflow

scifio/src/main/java/io/scif/util/MemoryTools.java

@@ -0,0 +1,61 @@
+/*
+ * #%L
+ * SCIFIO library for reading and converting scientific file formats.
+ * %%
+ * Copyright (C) 2011 - 2014 Board of Regents of the University of
+ * Wisconsin-Madison
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package io.scif.util;
+
+/**
+ * A utility class with convenience methods to obtain information about the
+ * heap.
+ * 
+ * @author Johannes Schindelin
+ */
+public class MemoryTools {
+
+	/**
+	 * Returns the total amount of remaining memory.
+	 * <p>
+	 * Slightly tricky: totalMemory() returns the amount of RAM claimed currently,
+	 * not the maximum amount Java will claim when asked (that is maxMemory()
+	 * instead). Likewise, freeMemory() returns the number of free bytes <i>in the
+	 * currently claimed chunk of RAM</i>, not the number of bytes still available
+	 * for Java.
+	 * <p>
+	 * </p>
+	 * Therefore, a little arithmetic is required to obtain the real number of
+	 * available bytes for us to use. </p>
+	 * 
+	 * @return the amount of memory available for data
+	 */
+	public static long totalAvailableMemory() {
+		final Runtime rt = Runtime.getRuntime();
+		return rt.freeMemory() + rt.maxMemory() - rt.totalMemory();
+	}
+
+}

scifio/src/test/java/io/scif/img/cell/cache/utests/CacheServiceTest.java

@@ -45,6 +45,7 @@
 import io.scif.img.cell.cache.CacheService;
 import io.scif.img.cell.loaders.ByteArrayLoader;
 import io.scif.img.cell.loaders.SCIFIOArrayLoader;
+import io.scif.util.MemoryTools;
 
 import java.io.IOException;
 import java.lang.ref.WeakReference;
@@ -496,7 +497,7 @@ private void enableCells(final boolean enabled, final SCIFIOCell<?>... cells)
 	 */
 	private void clearMem() {
 		if (arraySize == -1) {
-			arraySize = Runtime.getRuntime().freeMemory();
+			arraySize = MemoryTools.totalAvailableMemory();
 			if (arraySize > Integer.MAX_VALUE) {
 				arraySize = Integer.MAX_VALUE;
 			}

scifio/src/test/java/io/scif/img/cell/utests/SCIFIOCellImgTest.java

@@ -36,6 +36,7 @@
 import io.scif.img.IO;
 import io.scif.img.SCIFIOImgPlus;
 import io.scif.img.cell.SCIFIOCellImg;
+import io.scif.util.MemoryTools;
 
 import java.lang.ref.WeakReference;
 
@@ -84,7 +85,7 @@ public void testReaderCleanup() {
 //			new WeakReference<Metadata>(((SCIFIOCellImg) img.getImg()).reader()
 //				.getMetadata());
 //		img = null;
-//		long arraySize = Runtime.getRuntime().freeMemory();
+//		long arraySize = MemoryTools.totalAvailableMemory();
 //		if (arraySize > Integer.MAX_VALUE) {
 //			arraySize = Integer.MAX_VALUE;
 //		}