Omaha #3093 Add option to hprof tool to zero primitive arrays for compression.

Former-commit-id: 6a80964572cf331b433ae8dc222ac209dd35bf63

javaUtilities/com.raytheon.uf.viz.hprof/src/com/raytheon/hprof/BigByteBuffer.java

@@ -19,8 +19,8 @@
  **/
 package com.raytheon.hprof;
 
-import java.io.FileInputStream;
 import java.io.IOException;
+import java.io.RandomAccessFile;
 import java.nio.BufferUnderflowException;
 import java.nio.ByteBuffer;
 import java.nio.channels.FileChannel;
@@ -40,6 +40,7 @@ import java.nio.channels.FileChannel.MapMode;
  * Date          Ticket#  Engineer    Description
  * ------------- -------- ----------- --------------------------
  * Jan 08, 2014  2648     bsteffen    Initial doc
+ * May 20, 2014  3093     bsteffen    Allow read/write
  * 
  * </pre>
  * 
@@ -62,9 +63,12 @@ public class BigByteBuffer {
 
     private long limit;
 
-    public BigByteBuffer(String fileName) throws IOException {
+    public BigByteBuffer(String fileName, boolean readOnly) throws IOException {
-        FileInputStream fis = new FileInputStream(fileName);
+        String mode = readOnly ? "r" : "rw";
-        FileChannel fileChannel = fis.getChannel();
+        RandomAccessFile raf = null;
+        try {
+            raf = new RandomAccessFile(fileName, mode);
+            FileChannel fileChannel = raf.getChannel();
             offset = 0;
             limit = capacity = fileChannel.size();
             int nBuffers = (int) (capacity / chunkSize);
@@ -72,11 +76,16 @@ public class BigByteBuffer {
                 nBuffers += 1;
             }
             buffers = new ByteBuffer[nBuffers];
+            MapMode mapMode = readOnly ? MapMode.READ_ONLY : MapMode.READ_WRITE;
             for (int i = 0; i < buffers.length; i += 1) {
-            buffers[i] = fileChannel.map(MapMode.READ_ONLY, i * chunkSize,
+                buffers[i] = fileChannel.map(mapMode, i * chunkSize,
                         Math.min(capacity - i * chunkSize, chunkSize));
             }
-        fis.close();
+        } finally {
+            if (raf != null) {
+                raf.close();
+            }
+        }
     }
 
     protected BigByteBuffer(ByteBuffer[] buffers, long offset, long capacity) {
@@ -146,6 +155,17 @@ public class BigByteBuffer {
         return getBuffer(index).get(bufferIndex(index));
     }
 
+    public BigByteBuffer put(byte b) {
+        put(nextGetIndex(), b);
+        return this;
+    }
+
+    public BigByteBuffer put(long index, byte b) {
+        checkIndex(index);
+        getBuffer(index).put(bufferIndex(index), b);
+        return this;
+    }
+
     public void get(byte[] dst) {
         long start = nextGetIndex(dst.length);
         ByteBuffer buffer = getBuffer(start);

javaUtilities/com.raytheon.uf.viz.hprof/src/com/raytheon/hprof/HprofFile.java

@@ -51,6 +51,7 @@ import com.raytheon.hprof.data.heap.dump.InstanceDump;
  * Date          Ticket#  Engineer    Description
  * ------------- -------- ----------- --------------------------
  * Jan 08, 2014  2648     bsteffen    Initial doc
+ * May 20, 2014  3093     bsteffen    Allow opening for write.
  * 
  * </pre>
  * 
@@ -70,8 +71,8 @@ public class HprofFile {
 
     private Map<Id, String> usedClassnames = new HashMap<Id, String>();
 
-    public HprofFile(String fileName) throws IOException {
+    public HprofFile(String fileName, boolean readOnly) throws IOException {
-        BigByteBuffer buffer = new BigByteBuffer(fileName);
+        BigByteBuffer buffer = new BigByteBuffer(fileName, readOnly);
 
         String format = null;
 

javaUtilities/com.raytheon.uf.viz.hprof/src/com/raytheon/hprof/data/HeapDumpRecord.java

@@ -55,6 +55,7 @@ import com.raytheon.hprof.data.heap.root.RootThreadObject;
  * Date          Ticket#  Engineer    Description
  * ------------- -------- ----------- --------------------------
  * Jan 08, 2014  2648     bsteffen    Initial doc
+ * May 20, 2014  3093     bsteffen    Add zeroPrimitiveArrays
  * 
  * </pre>
  * 
@@ -137,12 +138,12 @@ public class HeapDumpRecord extends AbstractHprofRecord {
             }
             case ObjectArrayDump.TAG: {
                 objectArrays.add(buffer.position());
-                new ObjectArrayDump(buffer, idSize);
+                new ObjectArrayDump(buffer, idSize, false);
                 break;
             }
             case PrimitiveArrayDump.TAG: {
                 primitiveArrays.add(buffer.position());
-                new PrimitiveArrayDump(buffer, idSize);
+                new PrimitiveArrayDump(buffer, idSize, false);
                 break;
             }
             case HeapDumpSegmentRecord.TAG: {
@@ -234,7 +235,7 @@ public class HeapDumpRecord extends AbstractHprofRecord {
             return null;
         }
         buffer.position(index);
-        return new ObjectArrayDump(buffer, idSize);
+        return new ObjectArrayDump(buffer, idSize, true);
     }
 
     public BasicType[] getPrimitiveArray(Id objectId) {
@@ -243,7 +244,29 @@ public class HeapDumpRecord extends AbstractHprofRecord {
             return null;
         }
         buffer.position(index);
-        return new PrimitiveArrayDump(buffer, idSize).getArray();
+        return new PrimitiveArrayDump(buffer, idSize, true).getArray();
+    }
+
+    /**
+     * Zero out all data for non char primitive arrays in the backing file.
+     */
+    public void zeroPrimitiveArrays() {
+        for (long index : primitiveArraysById) {
+            buffer.position(index);
+            PrimitiveArrayDump dump = new PrimitiveArrayDump(buffer, idSize,
+                    true);
+            BasicType[] array = dump.getArray();
+            if (array.length > 0) {
+                BasicType sample = array[0];
+                if (!sample.isChar()) {
+                    int size = sample.getSize() * array.length;
+                    buffer.position(buffer.position() - size);
+                    for (int i = 0; i < size; i += 1) {
+                        buffer.put((byte) 0);
+                    }
+                }
+            }
+        }
     }
 
     private long binarySearch(long[] array, Id objectId) {

javaUtilities/com.raytheon.uf.viz.hprof/src/com/raytheon/hprof/data/heap/dump/ObjectArrayDump.java

@@ -34,6 +34,7 @@ import com.raytheon.hprof.data.HeapDumpRecord;
  * Date          Ticket#  Engineer    Description
  * ------------- -------- ----------- --------------------------
  * Jan 08, 2014  2648     bsteffen    Initial doc
+ * May 20, 2014  3093     bsteffen    Allow creation without reading full array.
  * 
  * </pre>
  * 
@@ -48,14 +49,19 @@ public class ObjectArrayDump extends AbstractDump {
 
     private final Id[] array;
 
-    public ObjectArrayDump(BigByteBuffer buffer, int idSize) {
+    public ObjectArrayDump(BigByteBuffer buffer, int idSize, boolean readArray) {
         super(buffer, idSize);
         int numElements = buffer.getInt();
         arrayClassId = new Id(buffer, idSize);
+        if (readArray) {
             array = new Id[numElements];
             for (int i = 0; i < numElements; i++) {
                 array[i] = new Id(buffer, idSize);
             }
+        } else {
+            array = null;
+            buffer.position(buffer.position() + idSize * numElements);
+        }
     }
 
     public Id[] getArray() {

javaUtilities/com.raytheon.uf.viz.hprof/src/com/raytheon/hprof/data/heap/dump/PrimitiveArrayDump.java

@@ -34,6 +34,7 @@ import com.raytheon.hprof.data.heap.BasicType;
  * Date          Ticket#  Engineer    Description
  * ------------- -------- ----------- --------------------------
  * Jan 08, 2014  2648     bsteffen    Initial doc
+ * May 20, 2014  3093     bsteffen    Allow creation without reading full array.
  * 
  * </pre>
  * 
@@ -46,14 +47,22 @@ public class PrimitiveArrayDump extends AbstractDump {
 
     private final BasicType[] array;
 
-    public PrimitiveArrayDump(BigByteBuffer buffer, int idSize) {
+    public PrimitiveArrayDump(BigByteBuffer buffer, int idSize,
+            boolean readArray) {
         super(buffer, idSize);
         int numElements = buffer.getInt();
         byte type = buffer.get();
+        if (readArray) {
             array = new BasicType[numElements];
             for (int i = 0; i < numElements; i++) {
                 array[i] = new BasicType(buffer, type, idSize);
             }
+        } else {
+            array = null;
+            BasicType tmp = new BasicType(buffer, type, idSize);
+            int skip = (numElements - 1) * tmp.getSize();
+            buffer.position(buffer.position() + skip);
+        }
     }
 
     public BasicType[] getArray() {

javaUtilities/com.raytheon.uf.viz.hprof/src/com/raytheon/uf/viz/hprof/CaveExporter.java

@@ -37,6 +37,7 @@ import com.raytheon.hprof.HprofFile;
  * ------------- -------- ----------- --------------------------
  * Jan 08, 2014  2648     bsteffen    Initial doc
  * May 05, 2014  3093     bsteffen    Add some new exporters
+ * May 20, 2014  3093     bsteffen    Add option to zero primitive arrays.
  * 
  * </pre>
  * 
@@ -51,17 +52,27 @@ public class CaveExporter {
                     .println("Provide some args, an hprof file is required, an output directory is optional.");
             System.exit(1);
         }
-        HprofFile hprof;
+        int argIdx = 0;
+        HprofFile hprof = null;
         try {
-            hprof = new HprofFile(args[0]);
+            if (args[argIdx].equals("-zero")) {
+                System.out.println("Writing 0s...");
+                hprof = new HprofFile(args[argIdx + 1], false);
+                hprof.getHeapDump().zeroPrimitiveArrays();
+                argIdx += 2;
+            } else {
+                hprof = new HprofFile(args[argIdx], true);
+                argIdx += 1;
+            }
+
         } catch (IOException e) {
             throw new IllegalArgumentException("Error opening hprof file: "
-                    + args[0], e);
+                    + args[argIdx], e);
         }
 
         File outputDir = null;
         if (args.length > 1) {
-            outputDir = new File(args[1]);
+            outputDir = new File(args[argIdx++]);
         } else {
             outputDir = new File(".");
         }