From 9267f7f233deff88f3fd511bfc3f8e4c6aaa5151 Mon Sep 17 00:00:00 2001
From: Radek Oslejsek <oslejsek@fi.muni.cz>
Date: Tue, 15 Feb 2022 15:19:57 +0100
Subject: [PATCH] Using Kryo with objenesis to accelerate serialization
---
Comparison/pom.xml | 12 ++-
.../cz/fidentis/analyst/face/HumanFace.java | 65 ++-----------
.../analyst/face/HumanFaceFactory.java | 93 ++++++++++++++++++-
.../batch/ApproxHausdorffDistTask.java | 2 +-
.../cz/fidentis/analyst/batch/BatchPanel.form | 27 ++++--
.../cz/fidentis/analyst/batch/BatchPanel.java | 32 +++++--
.../fidentis/analyst/batch/Bundle.properties | 1 +
7 files changed, 155 insertions(+), 77 deletions(-)
diff --git a/Comparison/pom.xml b/Comparison/pom.xml
index 6480685e..3135753c 100644
--- a/Comparison/pom.xml
+++ b/Comparison/pom.xml
@@ -85,9 +85,19 @@
<dependency>
<groupId>de.ruedigermoeller</groupId>
<artifactId>fst</artifactId>
- <version>2.57</version>
+ <version>3.0.3</version>
</dependency>
-->
+ <dependency>
+ <groupId>com.esotericsoftware</groupId>
+ <artifactId>kryo</artifactId>
+ <version>5.3.0</version>
+ </dependency>
+ <dependency>
+ <groupId>org.objenesis</groupId>
+ <artifactId>objenesis</artifactId>
+ <version>3.2</version>
+ </dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
diff --git a/Comparison/src/main/java/cz/fidentis/analyst/face/HumanFace.java b/Comparison/src/main/java/cz/fidentis/analyst/face/HumanFace.java
index 12707870..52e5700c 100644
--- a/Comparison/src/main/java/cz/fidentis/analyst/face/HumanFace.java
+++ b/Comparison/src/main/java/cz/fidentis/analyst/face/HumanFace.java
@@ -14,16 +14,10 @@ import cz.fidentis.analyst.visitors.face.HumanFaceVisitor;
import cz.fidentis.analyst.visitors.mesh.BoundingBox;
import cz.fidentis.analyst.visitors.mesh.BoundingBox.BBox;
import java.awt.image.BufferedImage;
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileInputStream;
-import java.io.FileOutputStream;
import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-import java.io.RandomAccessFile;
import java.io.Serializable;
import java.nio.file.Path;
import java.util.Collections;
@@ -66,7 +60,7 @@ public class HumanFace implements Serializable {
private final String id;
- private BufferedImage preview;
+ private transient BufferedImage preview;
/**
* Fast (de)serialization handler
@@ -140,6 +134,14 @@ public class HumanFace implements Serializable {
eventBus = new EventBus();
}
+ /**
+ * Non-public constructor necessary for the Kryo de-serialization
+ */
+ private HumanFace() {
+ id = null;
+ eventBus = new EventBus();
+ }
+
/**
* Returns the triangular mesh model of the human face.
*
@@ -407,55 +409,6 @@ public class HumanFace implements Serializable {
return null;
}
- /**
- * Creates serialized dump of the human face. Event buses are not stored.
- * Therefore, listeners have to re-register again after recovery.
- *
- * @return Dump file
- * @throws IOException on error in creating the dump file
- */
- public File dumpToFile() throws IOException {
- File tempFile = File.createTempFile(this.getClass().getSimpleName(), ".ser");
- tempFile.deleteOnExit();
- RandomAccessFile raf = new RandomAccessFile(tempFile, "rw");
-
- try (ObjectOutputStream fos = new ObjectOutputStream(new BufferedOutputStream(new FileOutputStream(raf.getFD())))) {
- fos.writeObject(this);
- fos.flush();
- }
-
- /*
- try (BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(tempFile))) {
- FSTObjectOutput out = FST_CONF.getObjectOutput(bos);
- out.writeObject(this, HumanFace.class);
- out.flush();
- }
- */
-
- return tempFile;
- }
-
- /**
- * Restores human face from a dump file.
- *
- * @param dumpFile The file
- * @return Human face
- * @throws IOException on error in reading the dump file
- * @throws java.lang.ClassNotFoundException on error when instantiating the human face
- */
- public static HumanFace restoreFromFile(File dumpFile) throws IOException, ClassNotFoundException {
- try (ObjectInputStream fos = new ObjectInputStream(new BufferedInputStream(new FileInputStream(dumpFile)))) {
- return (HumanFace) fos.readObject();
- }
- /*
- try (BufferedInputStream bis = new BufferedInputStream(new FileInputStream(dumpFile))) {
- FSTObjectInput in = FST_CONF.getObjectInput(bis);
- HumanFace face = (HumanFace) in.readObject(HumanFace.class);
- return face;
- }
- */
- }
-
/**
* Visits this face.
*
diff --git a/Comparison/src/main/java/cz/fidentis/analyst/face/HumanFaceFactory.java b/Comparison/src/main/java/cz/fidentis/analyst/face/HumanFaceFactory.java
index 176fd5da..85e3b9d8 100644
--- a/Comparison/src/main/java/cz/fidentis/analyst/face/HumanFaceFactory.java
+++ b/Comparison/src/main/java/cz/fidentis/analyst/face/HumanFaceFactory.java
@@ -1,12 +1,32 @@
package cz.fidentis.analyst.face;
+import com.esotericsoftware.kryo.Kryo;
+import com.esotericsoftware.kryo.io.Input;
+import com.esotericsoftware.kryo.io.Output;
+import com.esotericsoftware.kryo.util.DefaultInstantiatorStrategy;
+import cz.fidentis.analyst.Logger;
+import cz.fidentis.analyst.kdtree.KdNode;
+import cz.fidentis.analyst.kdtree.KdTree;
+import cz.fidentis.analyst.mesh.core.CornerTable;
+import cz.fidentis.analyst.mesh.core.CornerTableRow;
+import cz.fidentis.analyst.mesh.core.MeshFacetImpl;
+import cz.fidentis.analyst.mesh.core.MeshModel;
+import cz.fidentis.analyst.mesh.core.MeshPointImpl;
+import cz.fidentis.analyst.symmetry.Plane;
+import cz.fidentis.analyst.visitors.mesh.BoundingBox.BBox;
import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import java.util.SortedMap;
import java.util.TreeMap;
import java.util.logging.Level;
+import javax.vecmath.Point3d;
+import javax.vecmath.Vector3d;
+import org.objenesis.strategy.StdInstantiatorStrategy;
/**
* A flyweight factory that creates and caches human faces. Faces are
@@ -19,6 +39,8 @@ import java.util.logging.Level;
* @author Radek Oslejsek
*/
public class HumanFaceFactory {
+
+ private static Kryo kryo;
/**
* Memory clean up, i.e. dumping the file into disk and de-referencing it, is
@@ -82,7 +104,32 @@ public class HumanFaceFactory {
private Strategy strategy = Strategy.LRU;
private boolean reuseDumpFile = false;
-
+
+ /**
+ * Constructor.
+ */
+ public HumanFaceFactory() {
+ synchronized (this) {
+ if (HumanFaceFactory.kryo == null) {
+ HumanFaceFactory.kryo = new Kryo();
+ HumanFaceFactory.kryo.setInstantiatorStrategy(new DefaultInstantiatorStrategy(new StdInstantiatorStrategy()));
+ HumanFaceFactory.kryo.register(HumanFace.class);
+ HumanFaceFactory.kryo.register(MeshModel.class);
+ HumanFaceFactory.kryo.register(MeshFacetImpl.class);
+ HumanFaceFactory.kryo.register(MeshPointImpl.class);
+ HumanFaceFactory.kryo.register(CornerTable.class);
+ HumanFaceFactory.kryo.register(CornerTableRow.class);
+ HumanFaceFactory.kryo.register(BBox.class);
+ HumanFaceFactory.kryo.register(Plane.class);
+ HumanFaceFactory.kryo.register(KdTree.class);
+ HumanFaceFactory.kryo.register(KdNode.class);
+ HumanFaceFactory.kryo.register(Point3d.class);
+ HumanFaceFactory.kryo.register(Vector3d.class);
+ HumanFaceFactory.kryo.register(ArrayList.class);
+ HumanFaceFactory.kryo.register(HashMap.class);
+ }
+ }
+ }
/**
* Changes the dumping strategy
@@ -176,11 +223,12 @@ public class HumanFaceFactory {
// Free memory and recover human face from dump file:
HumanFace face;
try {
- face = HumanFace.restoreFromFile(dumpFile); // recover face from disk
+ face = restoreFromFile(dumpFile); // recover face from disk
checkMemAndDump(); // free the memory, if necessary
//System.out.println(face.getShortName() + " recovered");
- } catch (ClassNotFoundException|IOException ex) {
- java.util.logging.Logger.getLogger(HumanFaceFactory.class.getName()).log(Level.SEVERE, null, ex);
+ } catch (IOException ex) {
+ Logger.print("HumanFaceFactory ERROR: " + ex);
+ //java.util.logging.Logger.getLogger(HumanFaceFactory.class.getName()).log(Level.SEVERE, null, ex);
return null;
}
@@ -280,7 +328,7 @@ public class HumanFaceFactory {
HumanFace faceToDump = this.inMemoryFaces.remove(time);
this.usage.remove(faceToDump.getId());
if (!reuseDumpFile || !dumpedFaces.containsKey(faceToDump.getId())) { // dump only if it's required
- dumpedFaces.put(faceToDump.getId(), faceToDump.dumpToFile());
+ dumpedFaces.put(faceToDump.getId(), dumpToFile(faceToDump));
}
//System.out.println(faceToDump.getShortName() + " dumped");
}
@@ -304,4 +352,39 @@ public class HumanFaceFactory {
long allocatedMemory = (Runtime.getRuntime().totalMemory()-Runtime.getRuntime().freeMemory());
return Runtime.getRuntime().maxMemory() - allocatedMemory;
}
+
+ protected File dumpToFile(HumanFace face) throws IOException {
+ File tempFile = File.createTempFile(this.getClass().getSimpleName(), ".bin");
+ tempFile.deleteOnExit();
+
+ /*
+ RandomAccessFile raf = new RandomAccessFile(tempFile, "rw");
+ try (ObjectOutputStream fos = new ObjectOutputStream(new BufferedOutputStream(new FileOutputStream(raf.getFD())))) {
+ fos.writeObject(this);
+ fos.flush();
+ }
+ */
+
+ try (Output out = new Output(new FileOutputStream(tempFile))) {
+ kryo.writeObject(out, face);
+ } catch(Exception ex) {
+ throw new IOException(ex);
+ }
+
+ return tempFile;
+ }
+
+ protected static HumanFace restoreFromFile(File dumpFile) throws IOException {
+ /*
+ try (ObjectInputStream fos = new ObjectInputStream(new BufferedInputStream(new FileInputStream(dumpFile)))) {
+ return (HumanFace) fos.readObject();
+ }
+ */
+
+ try (Input in = new Input(new FileInputStream(dumpFile))) {
+ return kryo.readObject(in, HumanFace.class);
+ } catch(Exception ex) {
+ throw new IOException(ex);
+ }
+ }
}
diff --git a/GUI/src/main/java/cz/fidentis/analyst/batch/ApproxHausdorffDistTask.java b/GUI/src/main/java/cz/fidentis/analyst/batch/ApproxHausdorffDistTask.java
index f7666fbf..8cbb5965 100644
--- a/GUI/src/main/java/cz/fidentis/analyst/batch/ApproxHausdorffDistTask.java
+++ b/GUI/src/main/java/cz/fidentis/analyst/batch/ApproxHausdorffDistTask.java
@@ -96,7 +96,7 @@ public class ApproxHausdorffDistTask extends SimilarityTask {
HausdorffDistance.Strategy.POINT_TO_POINT,
true, // relative distance
true, // parallel
- true // crop
+ getControlPanel().getHdAutoCrop()
);
templateFace.getMeshModel().compute(hd);
distCache.add(hd.getDistances().values().stream() // Store relative distances of vertices to the cache
diff --git a/GUI/src/main/java/cz/fidentis/analyst/batch/BatchPanel.form b/GUI/src/main/java/cz/fidentis/analyst/batch/BatchPanel.form
index 44cfd207..aa6f9a1a 100644
--- a/GUI/src/main/java/cz/fidentis/analyst/batch/BatchPanel.form
+++ b/GUI/src/main/java/cz/fidentis/analyst/batch/BatchPanel.form
@@ -279,18 +279,20 @@
<Group type="102" attributes="0">
<EmptySpace max="-2" attributes="0"/>
<Group type="103" groupAlignment="0" attributes="0">
- <Group type="102" alignment="0" attributes="0">
- <Component id="jComboBox2" min="-2" max="-2" attributes="0"/>
- <EmptySpace max="-2" attributes="0"/>
- <Component id="jButtonInfo1" min="-2" max="-2" attributes="0"/>
- </Group>
<Group type="102" alignment="0" attributes="0">
<Component id="jButton4" min="-2" max="-2" attributes="0"/>
<EmptySpace type="unrelated" max="-2" attributes="0"/>
<Component id="jButton6" min="-2" max="-2" attributes="0"/>
</Group>
+ <Group type="102" alignment="0" attributes="0">
+ <Component id="jComboBox2" min="-2" max="-2" attributes="0"/>
+ <EmptySpace type="unrelated" max="-2" attributes="0"/>
+ <Component id="jCheckBox5" min="-2" max="-2" attributes="0"/>
+ <EmptySpace type="unrelated" max="-2" attributes="0"/>
+ <Component id="jButtonInfo1" min="-2" max="-2" attributes="0"/>
+ </Group>
</Group>
- <EmptySpace pref="359" max="32767" attributes="0"/>
+ <EmptySpace max="32767" attributes="0"/>
</Group>
</Group>
</DimensionLayout>
@@ -300,7 +302,10 @@
<EmptySpace min="-2" pref="14" max="-2" attributes="0"/>
<Group type="103" groupAlignment="0" max="-2" attributes="0">
<Component id="jButtonInfo1" max="32767" attributes="0"/>
- <Component id="jComboBox2" max="32767" attributes="0"/>
+ <Group type="103" groupAlignment="3" attributes="0">
+ <Component id="jComboBox2" alignment="3" max="32767" attributes="0"/>
+ <Component id="jCheckBox5" alignment="3" min="-2" max="-2" attributes="0"/>
+ </Group>
</Group>
<EmptySpace type="unrelated" max="-2" attributes="0"/>
<Group type="103" groupAlignment="3" attributes="0">
@@ -358,6 +363,14 @@
<Property name="enabled" type="boolean" value="false"/>
</Properties>
</Component>
+ <Component class="javax.swing.JCheckBox" name="jCheckBox5">
+ <Properties>
+ <Property name="selected" type="boolean" value="true"/>
+ <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
+ <ResourceString bundle="cz/fidentis/analyst/batch/Bundle.properties" key="BatchPanel.jCheckBox5.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, "{key}")"/>
+ </Property>
+ </Properties>
+ </Component>
</SubComponents>
</Container>
</SubComponents>
diff --git a/GUI/src/main/java/cz/fidentis/analyst/batch/BatchPanel.java b/GUI/src/main/java/cz/fidentis/analyst/batch/BatchPanel.java
index 955780a0..49ae71c1 100644
--- a/GUI/src/main/java/cz/fidentis/analyst/batch/BatchPanel.java
+++ b/GUI/src/main/java/cz/fidentis/analyst/batch/BatchPanel.java
@@ -124,6 +124,10 @@ public class BatchPanel extends ControlPanel {
return getStaticIcon();
}
+ public boolean getHdAutoCrop() {
+ return jCheckBox5.isSelected();
+ }
+
/**
* Sets the similarity export button
*
@@ -275,6 +279,11 @@ public class BatchPanel extends ControlPanel {
+ "<br/>"
+ "<strong>" + SIMILARITY_COMPLETE_HD + "</strong>: <br/>"
+ "Hausdorff distance is computed for all paris in both directions.<br/>"
+ + "<br/>"
+ + "<strong>HD auto-crop</strong>: <br/>"
+ + "If selected, then only overlapping parts of faces are included<br/>"
+ + "in the calculation of Hausdorff distance.<br/>"
+ + "<br/>"
+ "</html>",
"Distance computation strategies",
JOptionPane.INFORMATION_MESSAGE
@@ -330,6 +339,7 @@ public class BatchPanel extends ControlPanel {
jButton4 = new javax.swing.JButton();
jButtonInfo1 = new javax.swing.JButton();
jButton6 = new javax.swing.JButton();
+ jCheckBox5 = new javax.swing.JCheckBox();
setPreferredSize(new java.awt.Dimension(600, 600));
@@ -465,6 +475,9 @@ public class BatchPanel extends ControlPanel {
org.openide.awt.Mnemonics.setLocalizedText(jButton6, org.openide.util.NbBundle.getMessage(BatchPanel.class, "BatchPanel.jButton6.text")); // NOI18N
jButton6.setEnabled(false);
+ jCheckBox5.setSelected(true);
+ org.openide.awt.Mnemonics.setLocalizedText(jCheckBox5, org.openide.util.NbBundle.getMessage(BatchPanel.class, "BatchPanel.jCheckBox5.text")); // NOI18N
+
javax.swing.GroupLayout jPanel3Layout = new javax.swing.GroupLayout(jPanel3);
jPanel3.setLayout(jPanel3Layout);
jPanel3Layout.setHorizontalGroup(
@@ -472,15 +485,17 @@ public class BatchPanel extends ControlPanel {
.addGroup(jPanel3Layout.createSequentialGroup()
.addContainerGap()
.addGroup(jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
- .addGroup(jPanel3Layout.createSequentialGroup()
- .addComponent(jComboBox2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
- .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
- .addComponent(jButtonInfo1))
.addGroup(jPanel3Layout.createSequentialGroup()
.addComponent(jButton4)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
- .addComponent(jButton6)))
- .addContainerGap(359, Short.MAX_VALUE))
+ .addComponent(jButton6))
+ .addGroup(jPanel3Layout.createSequentialGroup()
+ .addComponent(jComboBox2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+ .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+ .addComponent(jCheckBox5)
+ .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
+ .addComponent(jButtonInfo1)))
+ .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
jPanel3Layout.setVerticalGroup(
jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
@@ -488,7 +503,9 @@ public class BatchPanel extends ControlPanel {
.addGap(14, 14, 14)
.addGroup(jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
.addComponent(jButtonInfo1, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
- .addComponent(jComboBox2))
+ .addGroup(jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
+ .addComponent(jComboBox2)
+ .addComponent(jCheckBox5)))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addGroup(jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jButton4)
@@ -547,6 +564,7 @@ public class BatchPanel extends ControlPanel {
private javax.swing.JCheckBox jCheckBox2;
private javax.swing.JCheckBox jCheckBox3;
private javax.swing.JCheckBox jCheckBox4;
+ private javax.swing.JCheckBox jCheckBox5;
private javax.swing.JComboBox<String> jComboBox1;
private javax.swing.JComboBox<String> jComboBox2;
private javax.swing.JLabel jLabel1;
diff --git a/GUI/src/main/resources/cz/fidentis/analyst/batch/Bundle.properties b/GUI/src/main/resources/cz/fidentis/analyst/batch/Bundle.properties
index abf208f3..514fde3e 100644
--- a/GUI/src/main/resources/cz/fidentis/analyst/batch/Bundle.properties
+++ b/GUI/src/main/resources/cz/fidentis/analyst/batch/Bundle.properties
@@ -17,3 +17,4 @@ BatchPanel.jLabel2.text=ICP undersampling (100% = none):
BatchPanel.jButton1.text=Compute
BatchPanel.jButtonInfo1.text=
BatchPanel.jButton6.text=Export results
+BatchPanel.jCheckBox5.text=HD auto-crop
--
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