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Switch from org.glassfish.jaxb:jaxb-runtime:2.3.3 to com.sun.xml.bind… #336

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merged 9 commits into from
Aug 21, 2024
Merged

Switch from org.glassfish.jaxb:jaxb-runtime:2.3.3 to com.sun.xml.bind… #336

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f71e927
Switch from org.glassfish.jaxb:jaxb-runtime:2.3.3 to com.sun.xml.bind…
calvertdw Aug 9, 2024
537b8fa
:arrow_up: ekf 0.7.8
calvertdw Aug 9, 2024
4110efd
Back IDLSequence.Byte with a ByteBuffer instead of a TByteArrayList.
calvertdw Aug 7, 2024
cc11104
:arrow_up: Low level libraries
calvertdw Aug 20, 2024
88adeab
Fix copying bytes.
calvertdw Aug 20, 2024
964b1fe
Fix copying bytes.
calvertdw Aug 20, 2024
59a726d
Generate messages.
calvertdw Aug 20, 2024
f0dedca
Revert message changes.
calvertdw Aug 20, 2024
b6b7182
:arrow_up: ihmc-robot-data-logger: 0.29.3
calvertdw Aug 21, 2024
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2 changes: 1 addition & 1 deletion example-simulations/build.gradle.kts
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Expand Up @@ -13,7 +13,7 @@ ihmc {
}

mainDependencies {
api("us.ihmc:ihmc-robot-data-logger:0.29.1")
api("us.ihmc:ihmc-robot-data-logger:0.29.3")
api("us.ihmc:ihmc-common-walking-control-modules:source")
api("us.ihmc:ihmc-whole-body-controller:source")

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2 changes: 1 addition & 1 deletion ihmc-avatar-interfaces/build.gradle.kts
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Expand Up @@ -19,7 +19,7 @@ mainDependencies {
api("com.hierynomus:sshj:0.32.0")

api("us.ihmc:mecano-graphviz:17-0.18.1")
api("us.ihmc:scs2-bullet-simulation:17-0.26.0")
api("us.ihmc:scs2-bullet-simulation:17-0.27.0")

api("us.ihmc:ihmc-humanoid-behaviors:source")
api("us.ihmc:ihmc-graphics-jmonkeyengine:source")
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2 changes: 1 addition & 1 deletion ...mc/avatar/networkProcessor/fiducialDetectorToolBox/FiducialDetectorToolboxController.java
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Expand Up @@ -137,7 +137,7 @@ public void updateInternal()

private void detectFromVideoPacket(VideoPacket videoPacket)
{
BufferedImage bufferedImage = jpegDecompressor.decompressJPEGDataToBufferedImage(videoPacket.getData().toArray());
BufferedImage bufferedImage = jpegDecompressor.decompressJPEGDataToBufferedImage(videoPacket.getData().copyArray());
detect(bufferedImage,
videoPacket.getPosition(),
videoPacket.getOrientation(),
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2 changes: 1 addition & 1 deletion ihmc-avatar-interfaces/src/main/java/us/ihmc/avatar/polaris/DRCVehicleSDFLoader.java
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Expand Up @@ -5,7 +5,7 @@
import java.net.MalformedURLException;
import java.util.ArrayList;

import javax.xml.bind.JAXBException;
import jakarta.xml.bind.JAXBException;

import us.ihmc.euclid.referenceFrame.ReferenceFrame;
import us.ihmc.euclid.referenceFrame.tools.ReferenceFrameTools;
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2 changes: 1 addition & 1 deletion ihmc-common-walking-control-modules/build.gradle.kts
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Expand Up @@ -31,7 +31,7 @@ testDependencies {
visualizersDependencies {
api(ihmc.sourceSetProject("main"))
api("us.ihmc:simulation-construction-set:0.25.1")
api("us.ihmc:scs2-simulation-construction-set:17-0.26.0")
api("us.ihmc:scs2-simulation-construction-set:17-0.27.0")

var javaFXVersion = "17.0.9"
api(ihmc.javaFXModule("base", javaFXVersion))
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4 changes: 2 additions & 2 deletions ihmc-communication/build.gradle.kts
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Expand Up @@ -15,7 +15,7 @@ ihmc {
mainDependencies {
api("us.ihmc:ihmc-realtime:1.6.0")
api("us.ihmc:ihmc-video-codecs:2.1.6")
api("us.ihmc:ihmc-ros2-library:0.24.2")
api("us.ihmc:ihmc-ros2-library:0.24.3")
api("org.boofcv:boofcv-geo:0.36")
api("commons-net:commons-net:3.6")
api("org.lz4:lz4-java:1.8.0")
Expand All @@ -27,5 +27,5 @@ mainDependencies {

testDependencies {
api("us.ihmc:ihmc-robotics-toolkit-test:source")
api("us.ihmc:ihmc-ros2-library-test:0.24.2")
api("us.ihmc:ihmc-ros2-library-test:0.24.3")
}
28 changes: 11 additions & 17 deletions ...tion/src/main/java/us/ihmc/communication/net/StereoVisionPointCloudMessageSerializer.java
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Expand Up @@ -11,6 +11,7 @@
import gnu.trove.list.array.TByteArrayList;
import us.ihmc.euclid.tuple3D.Point3D;
import us.ihmc.euclid.tuple4D.Quaternion;
import us.ihmc.idl.IDLSequence;

public class StereoVisionPointCloudMessageSerializer extends Serializer<StereoVisionPointCloudMessage>
{
Expand Down Expand Up @@ -41,8 +42,8 @@ public void write(Kryo kryo, Output output, StereoVisionPointCloudMessage object
output.writeDouble(pointCloudCenter.getZ());
output.writeDouble(object.getResolution());
output.writeInt(object.getNumberOfPoints(), true);
writeTByteList(object.getPointCloud());
writeTByteList(object.getColors());
writeByteSequence(object.getPointCloud());
writeByteSequence(object.getColors());
output.writeBoolean(object.getLz4Compressed());
}

Expand All @@ -62,15 +63,12 @@ public StereoVisionPointCloudMessage read(Kryo kryo, Input input, Class<? extend
message.getPointCloudCenter().set(input.readDouble(), input.readDouble(), input.readDouble());
message.setResolution(input.readDouble());
message.setNumberOfPoints(input.readInt(true));
readTByteList(message.getPointCloud());
readTByteList(message.getColors());
readByteSequence(message.getPointCloud());
readByteSequence(message.getColors());
message.setLz4Compressed(input.readBoolean());
return message;
}

private final Field tByteArrayListDataField = getField("_data");
private final Field tByteArrayListPosField = getField("_pos");

private static Field getField(String fieldName)
{
Field field;
Expand All @@ -86,30 +84,26 @@ private static Field getField(String fieldName)
}
}

private void writeTByteList(TByteArrayList list)
private void writeByteSequence(IDLSequence.Byte byteSequence)
{
output.writeInt(list.size(), true);
output.writeInt(byteSequence.size(), true);
try
{
byte[] data = (byte[]) tByteArrayListDataField.get(list);
output.write(data, 0, list.size());
output.write(byteSequence.getBuffer().array(), 0, byteSequence.size());
}
catch (Exception e)
{
throw new RuntimeException(e);
}
}

private void readTByteList(TByteArrayList list)
private void readByteSequence(IDLSequence.Byte byteSequence)
{
list.resetQuick();
byteSequence.resetQuick();
int size = input.readInt(true);
list.ensureCapacity(size);
try
{
byte[] data = (byte[]) tByteArrayListDataField.get(list);
input.read(data, 0, size);
tByteArrayListPosField.set(list, size);
input.read(byteSequence.getBuffer().array(), 0, size);
}
catch (Exception e)
{
Expand Down
6 changes: 3 additions & 3 deletions ...communication/src/main/java/us/ihmc/communication/packets/LidarPointCloudCompression.java
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@@ -1,9 +1,9 @@
package us.ihmc.communication.packets;

import perception_msgs.msg.dds.LidarScanMessage;
import gnu.trove.list.array.TByteArrayList;
import net.jpountz.lz4.LZ4Exception;
import us.ihmc.communication.compression.LZ4CompressionImplementation;
import us.ihmc.idl.IDLSequence;

import java.nio.ByteBuffer;
import java.nio.IntBuffer;
Expand Down Expand Up @@ -69,11 +69,11 @@ public static void compressPointCloud(int pointCloudSize, LidarScanMessage messa
messageToPack.setNumberOfPoints(pointCloudSize);
}

public static void decompressPointCloud(TByteArrayList compressedPointCloud,
public static void decompressPointCloud(IDLSequence.Byte compressedPointCloud,
int numberOfPoints,
LidarPointConsumer pointCoordinateConsumer)
{
ByteBuffer compressedPointCloudByteBuffer = ByteBuffer.wrap(compressedPointCloud.toArray());
ByteBuffer compressedPointCloudByteBuffer = compressedPointCloud.copyByteBuffer();
int numberOfDecompressedBytes = numberOfPoints * 4 * 3;
ByteBuffer decompressedPointCloudByteBuffer = ByteBuffer.allocate(numberOfDecompressedBytes);
compressorThreadLocal.get().decompress(compressedPointCloudByteBuffer, decompressedPointCloudByteBuffer, numberOfDecompressedBytes);
Expand Down
8 changes: 4 additions & 4 deletions ihmc-communication/src/main/java/us/ihmc/communication/packets/MessageTools.java
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Expand Up @@ -1080,7 +1080,7 @@ public static void packPrivilegedJointAngles(KinematicsToolboxPrivilegedConfigur

public static void packScan(LidarScanMessage lidarScanMessage, Point3DReadOnly[] scan)
{
lidarScanMessage.getScan().reset();
lidarScanMessage.getScan().resetQuick();
LidarPointCloudCompression.compressPointCloud(scan.length, lidarScanMessage, (i, j) -> scan[i].getElement(j));
}

Expand Down Expand Up @@ -1491,17 +1491,17 @@ public static Bool createBoolMessage(boolean data)
*/
public static void packLongStringToByteSequence(String longString, IDLSequence.Byte byteSequence)
{
byteSequence.clear();
byteSequence.resetQuick();
byte[] longStringBytes = longString.getBytes(StandardCharsets.US_ASCII);
byteSequence.addAll(longStringBytes);
byteSequence.add(longStringBytes);
}

/**
* See {@link #unpackLongStringFromByteSequence(IDLSequence.Byte)}.
*/
public static String unpackLongStringFromByteSequence(IDLSequence.Byte byteSequence)
{
byte[] longStringData = byteSequence.toArray();
byte[] longStringData = byteSequence.copyArray();
return new String(longStringData, StandardCharsets.US_ASCII);
}

Expand Down
73 changes: 24 additions & 49 deletions ...ommunication/src/main/java/us/ihmc/communication/packets/StereoPointCloudCompression.java
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Expand Up @@ -4,14 +4,14 @@
import java.nio.ByteBuffer;

import controller_msgs.msg.dds.StereoVisionPointCloudMessage;
import gnu.trove.list.array.TByteArrayList;
import net.jpountz.lz4.LZ4Exception;
import us.ihmc.communication.compression.LZ4CompressionImplementation;
import us.ihmc.euclid.tools.EuclidCoreTools;
import us.ihmc.euclid.tuple3D.Point3D;
import us.ihmc.euclid.tuple3D.Point3D32;
import us.ihmc.euclid.tuple3D.interfaces.Point3DBasics;
import us.ihmc.euclid.tuple3D.interfaces.Point3DReadOnly;
import us.ihmc.idl.IDLSequence;

/**
* This class should be used to create and unpack a {@link StereoVisionPointCloudMessage}.
Expand All @@ -31,8 +31,8 @@ public static class CompressionIntermediateVariablesPackage
private ByteBuffer rawColorByteBuffer;
private final LZ4CompressionImplementation compressor = new LZ4CompressionImplementation();

private ByteBufferedSequence byteBufferedPointCloud;
private ByteBufferedSequence byteBufferedColors;
private IDLSequence.Byte byteBufferedPointCloud;
private IDLSequence.Byte byteBufferedColors;
private ByteBuffer compressedPointCloudByteBuffer;
private ByteBuffer compressedColorByteBuffer;
private final StereoVisionPointCloudMessage message = new StereoVisionPointCloudMessage();
Expand All @@ -55,13 +55,13 @@ private void initialize(int numberOfPoints)
rawColorByteBuffer = ByteBuffer.allocate(colorByteBufferSize);

// LZ4 compression apparently needs some additional room to do its thing.
byteBufferedPointCloud = new ByteBufferedSequence(pointCloudByteBufferSize * 2, "type_9");
byteBufferedColors = new ByteBufferedSequence(colorByteBufferSize * 2, "type_9");
byteBufferedPointCloud = new IDLSequence.Byte(pointCloudByteBufferSize * 2, "type_9");
byteBufferedColors = new IDLSequence.Byte(colorByteBufferSize * 2, "type_9");

message.point_cloud_ = byteBufferedPointCloud;
message.colors_ = byteBufferedColors;
compressedPointCloudByteBuffer = byteBufferedPointCloud.byteBuffer;
compressedColorByteBuffer = byteBufferedColors.byteBuffer;
compressedPointCloudByteBuffer = byteBufferedPointCloud.getBuffer();
compressedColorByteBuffer = byteBufferedColors.getBuffer();
}
else
{
Expand All @@ -87,33 +87,8 @@ private void clearMessage()
message.getSensorOrientation().setToZero();
message.setResolution(0.0);
message.setNumberOfPoints(0);
message.getPointCloud().reset();
message.getColors().reset();
}
}

public static class ByteBufferedSequence extends us.ihmc.idl.IDLSequence.Byte
{
private ByteBuffer byteBuffer;

public ByteBufferedSequence(int maxSize, String typeCode)
{
super(maxSize, typeCode);
byteBuffer = ByteBuffer.wrap(this._data);
reset();
}

@Override
public void reset()
{
super.reset();
byteBuffer.clear();
byteBuffer.position(0);
}

public void setPosition(int position)
{
_pos = position;
message.getPointCloud().resetQuick();
message.getColors().resetQuick();
}
}

Expand Down Expand Up @@ -257,8 +232,8 @@ public static StereoVisionPointCloudMessage compressPointCloud(long timestamp,
colorByteBuffer.put(colorAccessor.getBlue(i));
}

variablesPackage.byteBufferedPointCloud.setPosition(variablesPackage.pointCloudByteBufferSize);
variablesPackage.byteBufferedColors.setPosition(variablesPackage.colorByteBufferSize);
variablesPackage.byteBufferedPointCloud.getBuffer().position(variablesPackage.pointCloudByteBufferSize);
variablesPackage.byteBufferedColors.getBuffer().position(variablesPackage.colorByteBufferSize);
}
else
{
Expand Down Expand Up @@ -303,8 +278,8 @@ public static StereoVisionPointCloudMessage compressPointCloud(long timestamp,
return null;
}

variablesPackage.byteBufferedPointCloud.setPosition(compressedPointCloudSize);
variablesPackage.byteBufferedColors.setPosition(compressedColorSize);
variablesPackage.byteBufferedPointCloud.getBuffer().position(compressedPointCloudSize);
variablesPackage.byteBufferedColors.getBuffer().position(compressedColorSize);
}

return message;
Expand All @@ -319,7 +294,7 @@ public static Point3D32[] decompressPointCloudToArray32(StereoVisionPointCloudMe
message.getLz4Compressed());
}

public static Point3D32[] decompressPointCloudToArray32(TByteArrayList compressedPointCloud,
public static Point3D32[] decompressPointCloudToArray32(IDLSequence.Byte compressedPointCloud,
Point3D center,
double resolution,
int numberOfPoints,
Expand All @@ -339,7 +314,7 @@ public static Point3D[] decompressPointCloudToArray(StereoVisionPointCloudMessag
message.getLz4Compressed());
}

public static Point3D[] decompressPointCloudToArray(TByteArrayList compressedPointCloud,
public static Point3D[] decompressPointCloudToArray(IDLSequence.Byte compressedPointCloud,
Point3D center,
double resolution,
int numberOfPoints,
Expand All @@ -360,7 +335,7 @@ public static void decompressPointCloud(StereoVisionPointCloudMessage message, P
pointCoordinateConsumer);
}

public static void decompressPointCloud(TByteArrayList compressedPointCloud,
public static void decompressPointCloud(IDLSequence.Byte compressedPointCloud,
Point3D center,
double resolution,
int numberOfPoints,
Expand All @@ -369,7 +344,7 @@ public static void decompressPointCloud(TByteArrayList compressedPointCloud,
{
if (isLZ4Compressed)
{
ByteBuffer compressedPointCloudByteBuffer = ByteBuffer.wrap(compressedPointCloud.toArray());
ByteBuffer compressedPointCloudByteBuffer = compressedPointCloud.copyByteBuffer();
ByteBuffer decompressedPointCloudByteBuffer = ByteBuffer.allocate(computePointByteBufferSize(numberOfPoints));
compressorThreadLocal.get().decompress(compressedPointCloudByteBuffer, decompressedPointCloudByteBuffer, computePointByteBufferSize(numberOfPoints));
decompressedPointCloudByteBuffer.flip();
Expand Down Expand Up @@ -405,7 +380,7 @@ public static Color[] decompressColorsToAWTColorArray(StereoVisionPointCloudMess
return decompressColorsToAWTColorArray(message.getColors(), message.getNumberOfPoints(), message.getLz4Compressed());
}

public static Color[] decompressColorsToAWTColorArray(TByteArrayList compressedColors, int numberOfPoints, boolean isLZ4Compressed)
public static Color[] decompressColorsToAWTColorArray(IDLSequence.Byte compressedColors, int numberOfPoints, boolean isLZ4Compressed)
{
Color[] colors = new Color[numberOfPoints];
decompressColors(compressedColors, numberOfPoints, isLZ4Compressed, ColorConsumer.toAWTColorArray(colors));
Expand All @@ -417,7 +392,7 @@ public static int[] decompressColorsToIntArray(StereoVisionPointCloudMessage mes
return decompressColorsToIntArray(message.getColors(), message.getNumberOfPoints(), message.getLz4Compressed());
}

public static int[] decompressColorsToIntArray(TByteArrayList compressedColors, int numberOfPoints, boolean isLZ4Compressed)
public static int[] decompressColorsToIntArray(IDLSequence.Byte compressedColors, int numberOfPoints, boolean isLZ4Compressed)
{
int[] colors = new int[numberOfPoints];
decompressColors(compressedColors, numberOfPoints, isLZ4Compressed, ColorConsumer.toRGBArray(colors));
Expand All @@ -429,11 +404,11 @@ public static void decompressColors(StereoVisionPointCloudMessage message, Color
decompressColors(message.getColors(), message.getNumberOfPoints(), message.getLz4Compressed(), colorConsumer);
}

public static void decompressColors(TByteArrayList compressedColors, int numberOfPoints, boolean isLZ4Compressed, ColorConsumer colorConsumer)
public static void decompressColors(IDLSequence.Byte compressedColors, int numberOfPoints, boolean isLZ4Compressed, ColorConsumer colorConsumer)
{
if (isLZ4Compressed)
{
ByteBuffer compressedColorByteBuffer = ByteBuffer.wrap(compressedColors.toArray());
ByteBuffer compressedColorByteBuffer = compressedColors.copyByteBuffer();
int colorByteBufferSize = computeColorByteBufferSize(numberOfPoints);
ByteBuffer decompressedColorByteBuffer = ByteBuffer.allocate(colorByteBufferSize);
compressorThreadLocal.get().decompress(compressedColorByteBuffer, decompressedColorByteBuffer, colorByteBufferSize);
Expand Down Expand Up @@ -729,9 +704,9 @@ public void accept(double x, double y, double z)
public static interface ColorConsumer
{
/**
* @param r the red component in the range (0 - 255).
* @param g the green component in the range (0 - 255).
* @param b the blue component in the range (0 - 255).
* @param red the red component in the range (0 - 255).
* @param green the green component in the range (0 - 255).
* @param blue the blue component in the range (0 - 255).
*/
void accept(int red, int blue, int green);

Expand Down
4 changes: 2 additions & 2 deletions ihmc-high-level-behaviors/build.gradle.kts
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Expand Up @@ -41,8 +41,8 @@ testDependencies {
api("us.ihmc:ihmc-graphics-libgdx-test:source")
api("us.ihmc:ihmc-path-planning-test:source")
api("org.cartesiantheatrics:bag-reader-java:0.0.1")
api("us.ihmc:scs2-examples:17-0.26.0")
api("us.ihmc:scs2-bullet-simulation-test:17-0.26.0")
api("us.ihmc:scs2-examples:17-0.27.0")
api("us.ihmc:scs2-bullet-simulation-test:17-0.27.0")
api("us.ihmc:example-simulations:source")
}

Expand Down
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