diff --git a/.gitignore b/.gitignore
index 3d47f986c41db29ec6dc0d5036bf760b3a1cf366..57f16fb67c1b1589981416b323d7a9debc728665 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,41 @@
-.idea/
+/build*
+/workspace
+setting.xml
+release/
target/
-.settings/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
+.idea/
+*.iws
*.iml
+*.ipr
+
+### Eclipse ###
+.apt_generated
+.classpath
+.factorypath
.project
-.classpath
\ No newline at end of file
+.settings
+.springBeans
+.sts4-cache
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/
+
+### Mac OS ###
+**/.DS_Store
+Icon?
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index b5f3b6e30928b9a4f9aa2d3dcf0095fcd13d3217..1c5d3b62b5f89f4dc74573706dae1925f87abdc0 100644
--- a/pom.xml
+++ b/pom.xml
@@ -8,18 +8,16 @@
<parent>
<artifactId>pom-icy</artifactId>
<groupId>org.bioimageanalysis.icy</groupId>
- <version>2.0.0</version>
+ <version>3.0.0-a.2</version>
</parent>
<!-- Project Information -->
<artifactId>opencv</artifactId>
- <version>4.5.1-2</version>
-
- <packaging>jar</packaging>
+ <version>5.0.0-a.1</version>
<name>OpenCV</name>
<description>OpenCV (Open Computer Vision) library for Icy. see more at http://opencv.org</description>
- <url>http://icy.bioimageanalysis.org/plugin/opencv/</url>
+ <url>https://icy.bioimageanalysis.org/plugin/opencv/</url>
<inceptionYear>2020</inceptionYear>
<organization>
@@ -52,79 +50,26 @@
</roles>
</developer>
</developers>
-
- <!-- Project properties -->
- <properties>
- <artifact-to-include>opencv</artifact-to-include>
- </properties>
-
- <profiles>
- <profile>
- <id>icy-plugin-extract-library</id>
- <activation>
- <activeByDefault>true</activeByDefault>
- </activation>
- </profile>
- </profiles>
-
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-dependency-plugin</artifactId>
- <executions>
- <execution>
- <id>${project.artifactId}-fetch</id>
- <phase>generate-sources</phase>
- <goals>
- <goal>unpack-dependencies</goal>
- </goals>
- <configuration>
- <includeArtifactIds>${artifact-to-include}</includeArtifactIds>
- <outputDirectory>${project.build.outputDirectory}</outputDirectory>
- <stripVersion>true</stripVersion>
- <excludeTransitive>true</excludeTransitive>
- </configuration>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>
<!-- List of project's dependencies -->
<dependencies>
<dependency>
<groupId>org.openpnp</groupId>
<artifactId>opencv</artifactId>
- <version>4.5.1-2</version>
- </dependency>
-
- <!-- The core of Icy -->
- <dependency>
- <groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>icy-kernel</artifactId>
- <version>${icy-kernel.version}</version>
+ <version>4.9.0-0</version>
</dependency>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>ezplug</artifactId>
- <version>${ezplug.version}</version>
</dependency>
-
- <dependency>
- <groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>icy-bioformats</artifactId>
- <version>${icy-bioformats.version}</version>
- </dependency>
</dependencies>
<!-- Icy Maven repository (to find parent POM) -->
<repositories>
<repository>
<id>icy</id>
- <name>Icy's Nexus</name>
- <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
</repository>
</repositories>
</project>
\ No newline at end of file
diff --git a/src/main/java/plugins/adufour/opencv/OpenCV.java b/src/main/java/plugins/adufour/opencv/OpenCV.java
index 473bb089b15fb290630d515f3c79d9a1e762c6e5..9ac4a1e801b80446fe52947fc1a4e7b19a23b1c1 100644
--- a/src/main/java/plugins/adufour/opencv/OpenCV.java
+++ b/src/main/java/plugins/adufour/opencv/OpenCV.java
@@ -1,48 +1,68 @@
+/*
+ * Copyright (c) 2010-2024. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.adufour.opencv;
+import org.bioimageanalysis.icy.Icy;
+import org.bioimageanalysis.icy.common.Version;
+import org.bioimageanalysis.icy.common.math.FPSMeter;
+import org.bioimageanalysis.icy.common.type.DataType;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImage;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.model.sequence.SequenceAdapter;
+import org.bioimageanalysis.icy.system.SystemUtil;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
+import org.opencv.core.Core;
+import org.opencv.core.CvType;
+import org.opencv.core.Mat;
+import org.opencv.core.Size;
+import org.opencv.imgproc.Imgproc;
+import org.opencv.videoio.VideoCapture;
+import org.opencv.videoio.Videoio;
+
+import javax.imageio.ImageIO;
import java.awt.image.BufferedImage;
import java.io.IOException;
import java.lang.reflect.Array;
import java.util.ArrayList;
import java.util.List;
+import java.util.Objects;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
-import javax.imageio.ImageIO;
-
-import org.opencv.core.Core;
-import org.opencv.core.CvType;
-import org.opencv.core.Mat;
-import org.opencv.core.Size;
-import org.opencv.imgproc.Imgproc;
-import org.opencv.videoio.VideoCapture;
-import org.opencv.videoio.Videoio;
-
-import icy.common.Version;
-import icy.image.IcyBufferedImage;
-import icy.main.Icy;
-import icy.math.FPSMeter;
-import icy.plugin.abstract_.Plugin;
-import icy.plugin.interface_.PluginLibrary;
-import icy.sequence.Sequence;
-import icy.sequence.SequenceAdapter;
-import icy.system.IcyExceptionHandler;
-import icy.system.IcyHandledException;
-import icy.system.SystemUtil;
-import icy.type.DataType;
-
/**
* <a href=http://opencv.org>OpenCV</a> library for Icy. This class contains additional test
* functions as well as tools to convert between OpenCV and Icy image formats.
- *
+ *
* @author Alexandre Dufour
*/
-public class OpenCV extends Plugin implements PluginLibrary
-{
- public static final Version OpenCV_Version = new Version(Core.VERSION_MAJOR, Core.VERSION_MINOR,
- Core.VERSION_REVISION);
+@IcyPluginName("OpenCV")
+@IcyPluginIcon(path = "/plugins/adufour/opencv/icon.png")
+public class OpenCV extends Plugin {
+ public static final Version OpenCV_Version = new Version(Core.VERSION_MAJOR, Core.VERSION_MINOR, Core.VERSION_REVISION);
/**
* A local buffer used to speed up repetitive conversions between OpenCV and Icy
@@ -51,41 +71,32 @@ public class OpenCV extends Plugin implements PluginLibrary
private static final ExecutorService service = Executors.newFixedThreadPool(SystemUtil.getNumberOfCPUs());
- static
- {
- String loadingMessage = "Loading OpenCV " + OpenCV_Version + "...";
- String successMessage = "OpenCV " + OpenCV_Version + " successfully loaded.";
+ static {
+ final String loadingMessage = "Loading OpenCV " + OpenCV_Version + "...";
+ final String successMessage = "OpenCV " + OpenCV_Version + " successfully loaded.";
- try
- {
+ try {
// First check whether OpenCV is already installed
- System.out.println(loadingMessage);
+ IcyLogger.info(OpenCV.class, loadingMessage);
nu.pattern.OpenCV.loadShared();
- System.out.println(successMessage);
+ IcyLogger.success(OpenCV.class, successMessage);
}
- catch (UnsatisfiedLinkError lib1)
- {
- IcyExceptionHandler.handleException(lib1, true);
- System.out.println("Trying alternate method");
+ catch (final UnsatisfiedLinkError lib1) {
+ IcyLogger.warn(OpenCV.class, lib1, "Unable to load OpenCV, trying alternate method (1/2)");
- try
- {
+ try {
// alternate method
loadLibrary(OpenCV.class, Core.NATIVE_LIBRARY_NAME);
}
- catch (UnsatisfiedLinkError lib2)
- {
- IcyExceptionHandler.handleException(lib2, true);
- System.out.println("Last chance...");
+ catch (final UnsatisfiedLinkError lib2) {
+ IcyLogger.warn(OpenCV.class, lib1, "Unable to load OpenCV, trying alternate method (2/2)");
- try
- {
+ try {
// last chance...
System.loadLibrary(Core.NATIVE_LIBRARY_NAME);
}
- catch (UnsatisfiedLinkError lib3)
- {
- IcyExceptionHandler.handleException(lib3, true);
+ catch (final UnsatisfiedLinkError lib3) {
+ IcyLogger.fatal(OpenCV.class, lib1, "Unable to load OpenCV");
}
}
}
@@ -95,22 +106,20 @@ public class OpenCV extends Plugin implements PluginLibrary
* Initializes OpenCV by loading the native libraries for the current operating system. This
* method should be called once before any OpenCV class is used
*/
- public static void initialize()
- {
+ @Contract(pure = true)
+ public static void initialize() {
// There is no need to actually initialize anything.
// The static block above will be executed as soon as this method is called.
}
/**
* Converts the specified OpenCV {@link Mat} into an {@link IcyBufferedImage}
- *
- * @param mat
- * the OpenCV {@link Mat} to convert
+ *
+ * @param mat the OpenCV {@link Mat} to convert
* @return an {@link IcyBufferedImage}
*/
- public static IcyBufferedImage convertToIcy(Mat mat)
- {
- IcyBufferedImage output = new IcyBufferedImage(mat.width(), mat.height(), mat.channels(), getIcyDataType(mat));
+ public static @NotNull IcyBufferedImage convertToIcy(final @NotNull Mat mat) {
+ final IcyBufferedImage output = new IcyBufferedImage(mat.width(), mat.height(), mat.channels(), Objects.requireNonNull(getIcyDataType(mat)));
convertToIcy(mat, output);
return output;
}
@@ -120,34 +129,32 @@ public class OpenCV extends Plugin implements PluginLibrary
* {@link IcyBufferedImage} object.<br>
* This method requires that the output image is initialized and has the correct dimensions and
* data type (if unsure, use {@link #convertToIcy(Mat)} instead).
- *
- * @param mat Mat
+ *
+ * @param mat Mat
* @param output IcyBufferedImage
- * throws {@link NullPointerException} if either parameter is null
+ * throws {@link NullPointerException} if either parameter is null
*/
- public static void convertToIcy(Mat mat, final IcyBufferedImage output)
- {
+ @SuppressWarnings({"SuspiciousSystemArraycopy", "JavaReflectionMemberAccess"})
+ public static void convertToIcy(final @NotNull Mat mat, final IcyBufferedImage output) {
final int width = mat.cols();
final int height = mat.rows();
final int nChannels = mat.channels();
- int bufferSize = width * height * nChannels;
+ final int bufferSize = width * height * nChannels;
// handle the easy case (single-channel) first
- if (nChannels == 1)
- {
- try
- {
+ if (nChannels == 1) {
+ try {
// Retrieve the frame data in a generic way
// This is equivalent to calling e.g. Mat.get(0, 0, (byte[]) buffer);
- Object dataBuffer = output.getDataXY(0);
- Class<?> dataType = dataBuffer.getClass();
+ final Object dataBuffer = output.getDataXY(0);
+ final Class<?> dataType = dataBuffer.getClass();
Mat.class.getMethod("get", int.class, int.class, dataType).invoke(mat, 0, 0, dataBuffer);
return;
}
- catch (Exception e)
- {
- throw new RuntimeException(e);
+ catch (final Exception e) {
+ IcyLogger.error(OpenCV.class, e);
+ return;
}
}
@@ -155,152 +162,130 @@ public class OpenCV extends Plugin implements PluginLibrary
if (Array.getLength(buffer) != bufferSize)
buffer = null;
final DataType dataType = getIcyDataType(mat);
- Class<?> type = dataType.toPrimitiveClass();
+ final Class<?> type = Objects.requireNonNull(dataType).toPrimitiveClass();
if (buffer == null || buffer.getClass().getComponentType() != type)
buffer = Array.newInstance(type, bufferSize);
- try
- {
+ try {
// Retrieve the frame data in a generic way
// This is equivalent to calling e.g. Mat.get(0, 0, (byte[]) buffer);
Mat.class.getMethod("get", int.class, int.class, buffer.getClass()).invoke(mat, 0, 0, buffer);
}
- catch (Exception e)
- {
- throw new RuntimeException(e);
+ catch (final Exception e) {
+ IcyLogger.error(OpenCV.class, e);
+ return;
}
- ArrayList<Future<?>> tasks = new ArrayList<Future<?>>(nChannels);
+ final ArrayList<Future<?>> tasks = new ArrayList<>(nChannels);
- for (int c = 0; c < nChannels; c++)
- {
+ for (int c = 0; c < nChannels; c++) {
final int channel = c;
- tasks.add(service.submit(new Runnable()
- {
- @Override
- public void run()
- {
- switch (dataType)
- {
- case BYTE:
- case UBYTE:
- {
- // OpenCV reads BGR by default => revert this to conventional RGB
- final byte[] icyChannel = output.getDataXYAsByte(nChannels - channel - 1);
- for (int out = 0, in = channel; out < icyChannel.length; out++, in += nChannels)
- icyChannel[out] = ((byte[]) buffer)[in];
- break;
- }
- case SHORT:
- case USHORT:
- {
- // OpenCV reads BGR by default => revert this to conventional RGB
- final short[] icyChannel = output.getDataXYAsShort(nChannels - channel - 1);
- for (int out = 0, in = channel; out < icyChannel.length; out++, in += nChannels)
- icyChannel[out] = ((short[]) buffer)[in];
- break;
- }
- case INT:
- {
- // OpenCV reads BGR by default => revert this to conventional RGB
- final int[] icyChannel = output.getDataXYAsInt(nChannels - channel - 1);
- for (int out = 0, in = channel; out < icyChannel.length; out++, in += nChannels)
- icyChannel[out] = ((int[]) buffer)[in];
- break;
- }
- case FLOAT:
- {
- // OpenCV reads BGR by default => revert this to conventional RGB
- final float[] icyChannel = output.getDataXYAsFloat(nChannels - channel - 1);
- for (int out = 0, in = channel; out < icyChannel.length; out++, in += nChannels)
- icyChannel[out] = ((float[]) buffer)[in];
- break;
- }
- case DOUBLE:
- {
- // OpenCV reads BGR by default => revert this to conventional RGB
- final double[] icyChannel = output.getDataXYAsDouble(nChannels - channel - 1);
- for (int out = 0, in = channel; out < icyChannel.length; out++, in += nChannels)
- icyChannel[out] = ((double[]) buffer)[in];
- break;
- }
- default:
- {
- // OpenCV reads BGR by default => revert this to conventional RGB
- final Object icyChannel = output.getDataXY(nChannels - channel - 1);
- int size = Array.getLength(icyChannel);
- for (int out = 0, in = channel; out < size; out++, in += nChannels)
- System.arraycopy(buffer, in, icyChannel, out, 1);
- }
+ tasks.add(service.submit(() -> {
+ switch (dataType) {
+ case BYTE:
+ case UBYTE: {
+ // OpenCV reads BGR by default => revert this to conventional RGB
+ final byte[] icyChannel = output.getDataXYAsByte(nChannels - channel - 1);
+ for (int out = 0, in = channel; out < icyChannel.length; out++, in += nChannels)
+ icyChannel[out] = ((byte[]) buffer)[in];
+ break;
+ }
+ case SHORT:
+ case USHORT: {
+ // OpenCV reads BGR by default => revert this to conventional RGB
+ final short[] icyChannel = output.getDataXYAsShort(nChannels - channel - 1);
+ for (int out = 0, in = channel; out < icyChannel.length; out++, in += nChannels)
+ icyChannel[out] = ((short[]) buffer)[in];
+ break;
+ }
+ case INT: {
+ // OpenCV reads BGR by default => revert this to conventional RGB
+ final int[] icyChannel = output.getDataXYAsInt(nChannels - channel - 1);
+ for (int out = 0, in = channel; out < icyChannel.length; out++, in += nChannels)
+ icyChannel[out] = ((int[]) buffer)[in];
+ break;
+ }
+ case FLOAT: {
+ // OpenCV reads BGR by default => revert this to conventional RGB
+ final float[] icyChannel = output.getDataXYAsFloat(nChannels - channel - 1);
+ for (int out = 0, in = channel; out < icyChannel.length; out++, in += nChannels)
+ icyChannel[out] = ((float[]) buffer)[in];
+ break;
+ }
+ case DOUBLE: {
+ // OpenCV reads BGR by default => revert this to conventional RGB
+ final double[] icyChannel = output.getDataXYAsDouble(nChannels - channel - 1);
+ for (int out = 0, in = channel; out < icyChannel.length; out++, in += nChannels)
+ icyChannel[out] = ((double[]) buffer)[in];
+ break;
+ }
+ default: {
+ // OpenCV reads BGR by default => revert this to conventional RGB
+ final Object icyChannel = output.getDataXY(nChannels - channel - 1);
+ final int size = Array.getLength(icyChannel);
+ for (int out = 0, in = channel; out < size; out++, in += nChannels)
+ System.arraycopy(buffer, in, icyChannel, out, 1);
}
}
}));
}
- try
- {
- for (Future<?> task : tasks)
+ try {
+ for (final Future<?> task : tasks)
task.get();
}
- catch (InterruptedException e)
- {
+ catch (final InterruptedException e) {
Thread.currentThread().interrupt();
}
- catch (ExecutionException e)
- {
- e.printStackTrace();
+ catch (final ExecutionException e) {
+ IcyLogger.error(OpenCV.class, e);
}
}
/**
* Converts the specified {@link IcyBufferedImage} into an OpenCV {@link Mat}
- *
- * @param img
- * the {@link IcyBufferedImage} to convert
+ *
+ * @param img the {@link IcyBufferedImage} to convert
* @return an OpenCV {@link Mat}
*/
- public static Mat convertToOpenCV(IcyBufferedImage img)
- {
- int width = img.getWidth();
- int height = img.getHeight();
- int sizeC = img.getSizeC();
- int bufferSize = width * height * sizeC;
+ @SuppressWarnings({"SuspiciousSystemArraycopy", "JavaReflectionMemberAccess"})
+ public static @Nullable Mat convertToOpenCV(final @NotNull IcyBufferedImage img) {
+ final int width = img.getWidth();
+ final int height = img.getHeight();
+ final int sizeC = img.getSizeC();
+ final int bufferSize = width * height * sizeC;
- Mat mat = new Mat(new Size(width, height), getCVDataType(img));
+ final Mat mat = new Mat(new Size(width, height), getCVDataType(img));
- if (sizeC == 1)
- {
+ if (sizeC == 1) {
buffer = img.getDataXY(0);
}
- else
- {
+ else {
// Make sure the buffer has the proper type and size
if (Array.getLength(buffer) != bufferSize)
buffer = null;
- Class<?> type = img.getDataType_().toPrimitiveClass();
+ final Class<?> type = img.getDataType().toPrimitiveClass();
if (buffer == null || buffer.getClass().getComponentType() != type)
buffer = Array.newInstance(type, bufferSize);
- for (int c = 0; c < sizeC; c++)
- {
+ for (int c = 0; c < sizeC; c++) {
// OpenCV Mat elements are interleaved...
- Object in = img.getDataXY(sizeC - c - 1);
+ final Object in = img.getDataXY(sizeC - c - 1);
for (int j = 0, offIN = 0, offOUT = c; j < height; j++)
for (int i = 0; i < width; i++, offIN++, offOUT += sizeC)
System.arraycopy(in, offIN, buffer, offOUT, 1);
}
}
- try
- {
+ try {
// Retrieve the frame data in a generic way
// This is equivalent to calling e.g. Mat.put(0, 0, (byte[]) buffer);
Mat.class.getMethod("put", int.class, int.class, buffer.getClass()).invoke(mat, 0, 0, buffer);
}
- catch (Exception e)
- {
- throw new RuntimeException(e);
+ catch (final Exception e) {
+ IcyLogger.error(OpenCV.class, e);
+ return null;
}
return mat;
@@ -309,57 +294,37 @@ public class OpenCV extends Plugin implements PluginLibrary
/**
* @param img Icy Buffered Image
* @return the OpenCV data type corresponding to the specified image (see the {@link CvType}
- * .CV_* constants)
+ * .CV_* constants)
*/
- public static int getCVDataType(IcyBufferedImage img)
- {
- switch (img.getDataType_())
- {
- case BYTE:
- return CvType.CV_8SC(img.getSizeC());
- case UBYTE:
- return CvType.CV_8UC(img.getSizeC());
- case SHORT:
- return CvType.CV_16SC(img.getSizeC());
- case USHORT:
- return CvType.CV_16UC(img.getSizeC());
- case UINT: // TODO ?
- case INT:
- return CvType.CV_32SC(img.getSizeC());
- case FLOAT:
- return CvType.CV_32FC(img.getSizeC());
- case DOUBLE:
- return CvType.CV_64FC(img.getSizeC());
- default:
- throw new UnsupportedOperationException("OpenCV does not support type " + img.getDataType_());
- }
+ public static int getCVDataType(final @NotNull IcyBufferedImage img) {
+ return switch (img.getDataType()) {
+ case BYTE -> CvType.CV_8SC(img.getSizeC());
+ case UBYTE -> CvType.CV_8UC(img.getSizeC());
+ case SHORT -> CvType.CV_16SC(img.getSizeC());
+ case USHORT -> CvType.CV_16UC(img.getSizeC());
+ case UINT // TODO ?
+ , INT -> CvType.CV_32SC(img.getSizeC());
+ case FLOAT -> CvType.CV_32FC(img.getSizeC());
+ case DOUBLE -> CvType.CV_64FC(img.getSizeC());
+ default -> throw new UnsupportedOperationException("OpenCV does not support type " + img.getDataType());
+ };
}
/**
* @param mat Mat
* @return the {@link DataType} corresponding to the specified OpenCV {@link Mat}rix
*/
- public static DataType getIcyDataType(Mat mat)
- {
- switch (CvType.depth(mat.type()))
- {
- case CvType.CV_8S:
- return DataType.BYTE;
- case CvType.CV_8U:
- return DataType.UBYTE;
- case CvType.CV_16S:
- return DataType.SHORT;
- case CvType.CV_16U:
- return DataType.USHORT;
- case CvType.CV_32S:
- return DataType.INT;
- case CvType.CV_32F:
- return DataType.FLOAT;
- case CvType.CV_64F:
- return DataType.DOUBLE;
- default:
- return null;
- }
+ public static @Nullable DataType getIcyDataType(final @NotNull Mat mat) {
+ return switch (CvType.depth(mat.type())) {
+ case CvType.CV_8S -> DataType.BYTE;
+ case CvType.CV_8U -> DataType.UBYTE;
+ case CvType.CV_16S -> DataType.SHORT;
+ case CvType.CV_16U -> DataType.USHORT;
+ case CvType.CV_32S -> DataType.INT;
+ case CvType.CV_32F -> DataType.FLOAT;
+ case CvType.CV_64F -> DataType.DOUBLE;
+ default -> null;
+ };
}
/**
@@ -367,8 +332,7 @@ public class OpenCV extends Plugin implements PluginLibrary
* viewer. This method will run indefinitely unless the viewer is closed or its calling thread
* is interrupted (see {@link Thread#interrupt()})
*/
- public static void liveWebcam()
- {
+ public static void liveWebcam() {
liveWebcam(-1, -1, -1);
}
@@ -377,14 +341,13 @@ public class OpenCV extends Plugin implements PluginLibrary
* viewer. This method will run indefinitely unless the viewer is closed or its calling thread
* is interrupted (see {@link Thread#interrupt()})
*
- * @param width int
+ * @param width int
* @param height int
- * @param fps int
+ * @param fps int
*/
- public static void liveWebcam(final int width, final int height, final int fps)
- {
+ public static void liveWebcam(final int width, final int height, final int fps) {
// Connect to the camera
- VideoCapture vc = new VideoCapture(0);
+ final VideoCapture vc = new VideoCapture(0);
if (width != -1)
vc.set(Videoio.CAP_PROP_FRAME_WIDTH, width);
if (height != -1)
@@ -400,20 +363,17 @@ public class OpenCV extends Plugin implements PluginLibrary
* viewer. This method will run indefinitely unless the viewer is closed or its calling thread
* is interrupted (see {@link Thread#interrupt()})
*/
- public static void liveWebcam(final VideoCapture camera)
- {
- new Thread(new Runnable()
- {
+ public static void liveWebcam(final VideoCapture camera) {
+ new Thread(new Runnable() {
@Override
- public void run()
- {
+ public void run() {
// We need to know which thread to interrupt to clean the camera
final Thread currentThread = Thread.currentThread();
// Read the first image to initialize the meta-data
- Mat mat = new Mat();
+ final Mat mat = new Mat();
camera.read(mat);
- IcyBufferedImage image = convertToIcy(mat);
+ final IcyBufferedImage image = convertToIcy(mat);
// Create the sequence
final Sequence s = new Sequence("Live webcam", image);
@@ -424,19 +384,16 @@ public class OpenCV extends Plugin implements PluginLibrary
s.setAutoUpdateChannelBounds(false);
// Closing the sequence should stop the camera
- s.addListener(new SequenceAdapter()
- {
+ s.addListener(new SequenceAdapter() {
@Override
- public void sequenceClosed(Sequence sequence)
- {
+ public void sequenceClosed(final Sequence sequence) {
s.removeListener(this);
currentThread.interrupt();
}
});
- try
- {
- FPSMeter fps = new FPSMeter();
+ try {
+ final FPSMeter fps = new FPSMeter();
long grabTime = 0;
long readTime = 0;
long conversionTime = 0;
@@ -444,17 +401,16 @@ public class OpenCV extends Plugin implements PluginLibrary
double nbIterations = 0.0;
// loop until the thread is interrupted
- while (!currentThread.isInterrupted())
- {
- long t0 = System.nanoTime();
+ while (!currentThread.isInterrupted()) {
+ final long t0 = System.nanoTime();
camera.grab();
- long t1 = System.nanoTime();
+ final long t1 = System.nanoTime();
camera.retrieve(mat);
- long t2 = System.nanoTime();
+ final long t2 = System.nanoTime();
convertToIcy(mat, image);
- long t3 = System.nanoTime();
+ final long t3 = System.nanoTime();
image.dataChanged();
- long t4 = System.nanoTime();
+ final long t4 = System.nanoTime();
fps.update();
nbIterations++;
@@ -463,14 +419,13 @@ public class OpenCV extends Plugin implements PluginLibrary
conversionTime += (t3 - t2) / 1000000;
dataUpdateTime += (t4 - t3) / 1000000;
}
- System.out.println("Capture frame-rate: " + fps.getFPS() + " fps");
- System.out.println("Camera grab time: " + grabTime / nbIterations + " ms");
- System.out.println("Camera read time: " + readTime / nbIterations + " ms");
- System.out.println("Conversion time: " + conversionTime / nbIterations + " ms");
- System.out.println("Data update time: " + dataUpdateTime / nbIterations + " ms");
+ IcyLogger.info(OpenCV.class, "Capture frame-rate: " + fps.getFPS() + " fps");
+ IcyLogger.info(OpenCV.class, "Camera grab time: " + grabTime / nbIterations + " ms");
+ IcyLogger.info(OpenCV.class, "Camera read time: " + readTime / nbIterations + " ms");
+ IcyLogger.info(OpenCV.class, "Conversion time: " + conversionTime / nbIterations + " ms");
+ IcyLogger.info(OpenCV.class, "Data update time: " + dataUpdateTime / nbIterations + " ms");
}
- finally
- {
+ finally {
// close the camera
camera.release();
}
@@ -482,32 +437,30 @@ public class OpenCV extends Plugin implements PluginLibrary
* OpenCV test that takes the active image and performs a Sobel filter in X and Y and combines
* the result into a new image
*/
- public static void testSobel()
- {
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- Sequence s = Icy.getMainInterface().getActiveSequence();
+ public static void testSobel() {
+ new Thread(() -> {
+ Sequence s = Icy.getMainInterface().getActiveSequence();
+
+ if (s == null) {
+ IcyLogger.error(OpenCV.class, "Open an image first!");
+ return;
+ }
- if (s == null)
- throw new IcyHandledException("Open an image first!");
+ final Mat mat = convertToOpenCV(Icy.getMainInterface().getActiveImage());
- Mat mat = convertToOpenCV(Icy.getMainInterface().getActiveImage());
+ final Mat x = new Mat();
+ final Mat y = new Mat();
- Mat x = new Mat();
- Mat y = new Mat();
+ Objects.requireNonNull(mat);
- Imgproc.Sobel(mat, x, -1, 1, 0);
- Imgproc.Sobel(mat, y, -1, 0, 1);
+ Imgproc.Sobel(mat, x, -1, 1, 0);
+ Imgproc.Sobel(mat, y, -1, 0, 1);
- org.opencv.core.Core.addWeighted(x, 0.5, y, 0.5, 1.0, mat);
+ Core.addWeighted(x, 0.5, y, 0.5, 1.0, mat);
- s = new Sequence("OpenCV: Sobel filter applied to " + s.getName(), convertToIcy(mat));
+ s = new Sequence("OpenCV: Sobel filter applied to " + s.getName(), convertToIcy(mat));
- Icy.getMainInterface().addSequence(s);
- }
+ Icy.getMainInterface().addSequence(s);
}).start();
}
@@ -518,28 +471,24 @@ public class OpenCV extends Plugin implements PluginLibrary
* RPiCamera's encoding setting (JPEG by default).<br>
* <br>
* Usage Example:<br>
- *
+ *
* <pre>
* BufferedImage buffImg = piCamera.takeBufferedStill(500, 500);
* </pre>
- *
- * @param width
- * An int specifying width of image to take.
- * @param height
- * An int specifying height of image to take.
+ *
+ * @param width An int specifying width of image to take.
+ * @param height An int specifying height of image to take.
* @return A BufferedImage containing the image.
- * @throws IOException
- * this exception is thrown if:
- * <ul>
- * <li>The system is not a Raspberry Pi (RPi),</li>
- * <li>The RPi is not equipped with a camera board,</li>
- * <li>The <code>raspistill</code> utility is not installed,</li>
- * <li>Something went wrong when reading the image from the camera</li>
- * </ul>
+ * @throws IOException this exception is thrown if:
+ * <ul>
+ * <li>The system is not a Raspberry Pi (RPi),</li>
+ * <li>The RPi is not equipped with a camera board,</li>
+ * <li>The <code>raspistill</code> utility is not installed,</li>
+ * <li>Something went wrong when reading the image from the camera</li>
+ * </ul>
*/
- public static BufferedImage rpi_raspistillToBufferedImage(int width, int height) throws IOException
- {
- List<String> command = new ArrayList<String>();
+ public static BufferedImage rpi_raspistillToBufferedImage(final int width, final int height) throws IOException {
+ final List<String> command = new ArrayList<>();
command.add("raspistill");
command.add("-o");
command.add("-v");
@@ -547,7 +496,7 @@ public class OpenCV extends Plugin implements PluginLibrary
command.add("" + width);
command.add("-h");
command.add("" + height);
- ProcessBuilder pb = new ProcessBuilder(command);
+ final ProcessBuilder pb = new ProcessBuilder(command);
// System.out.println("Executed this command:\n\t" + command.toString());
// pb.redirectErrorStream(true);
@@ -555,8 +504,7 @@ public class OpenCV extends Plugin implements PluginLibrary
// new File(System.getProperty("user.home") + File.separator +
// "Desktop" + File.separator + "RPiCamera.out"));
- Process p = pb.start();
- BufferedImage bi = ImageIO.read(p.getInputStream());
+ final Process p = pb.start();
// --------------------------------------------------------------------------
// This code can be used to specify an ImageReader - perhaps for a specific
// type of image - in place of the previous line:
@@ -568,7 +516,7 @@ public class OpenCV extends Plugin implements PluginLibrary
// ImageReadParam param = reader.getDefaultReadParam();
// BufferedImage bi = reader.read(0, param);
// --------------------------------------------------------------------------
- return bi;
+ return ImageIO.read(p.getInputStream());
}
}
diff --git a/src/main/java/plugins/adufour/opencv/OpenCVCapture.java b/src/main/java/plugins/adufour/opencv/OpenCVCapture.java
index 0e3f23435333891c6c8715c4eff9d07de013e1bc..5fa6d22ab6e092dcdd7e6092137587837b1df0ea 100644
--- a/src/main/java/plugins/adufour/opencv/OpenCVCapture.java
+++ b/src/main/java/plugins/adufour/opencv/OpenCVCapture.java
@@ -1,40 +1,54 @@
-package plugins.adufour.opencv;
-
-import java.lang.reflect.Field;
-import java.util.ArrayList;
-import java.util.List;
+/*
+ * Copyright (c) 2010-2024. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import javax.swing.JSeparator;
+package plugins.adufour.opencv;
+import org.bioimageanalysis.icy.Icy;
+import org.bioimageanalysis.icy.common.math.FPSMeter;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImage;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.model.sequence.SequenceAdapter;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
import org.opencv.core.Mat;
import org.opencv.videoio.VideoCapture;
import org.opencv.videoio.Videoio;
-
-import icy.image.IcyBufferedImage;
-import icy.main.Icy;
-import icy.math.FPSMeter;
-import icy.sequence.Sequence;
-import icy.sequence.SequenceAdapter;
-import plugins.adufour.ezplug.EzPlug;
-import plugins.adufour.ezplug.EzStoppable;
-import plugins.adufour.ezplug.EzVar;
-import plugins.adufour.ezplug.EzVarInteger;
-import plugins.adufour.ezplug.EzVarListener;
+import plugins.adufour.ezplug.*;
import plugins.adufour.vars.util.VarException;
-public class OpenCVCapture extends EzPlug implements EzStoppable, EzVarListener<Integer>
-{
- List<EzVarInteger> parameters = new ArrayList<EzVarInteger>();
-
+import javax.swing.*;
+import java.lang.reflect.Field;
+import java.util.ArrayList;
+import java.util.List;
+
+@IcyPluginName("OpenCV Capture")
+@IcyPluginIcon(path = "/plugins/adufour/opencv/icon.png")
+public class OpenCVCapture extends EzPlug implements EzStoppable, EzVarListener<Integer> {
+ List<EzVarInteger> parameters = new ArrayList<>();
+
VideoCapture camera = null;
-
+
@Override
- protected void initialize()
- {
+ protected void initialize() {
OpenCV.initialize();
-
- for (Field f : Videoio.class.getDeclaredFields())
- {
+
+ for (final Field f : Videoio.class.getDeclaredFields()) {
String name = f.getName();
if (!name.startsWith("CAP_PROP_")) continue;
if (name.contains("_DC1394")) continue;
@@ -47,114 +61,99 @@ public class OpenCVCapture extends EzPlug implements EzStoppable, EzVarListener<
if (name.contains("_POS")) continue;
if (name.contains("_PVAPI")) continue;
if (name.contains("_XI")) continue;
-
+
name = name.substring(9).toLowerCase();
- EzVarInteger setting = new EzVarInteger(name);
- setting.setValue(Integer.valueOf(-1));
+ final EzVarInteger setting = new EzVarInteger(name);
+ setting.setValue(-1);
setting.addVarChangeListener(this);
parameters.add(setting);
}
-
+
int cpt = 0;
- for (EzVarInteger setting : parameters)
- {
+ for (final EzVarInteger setting : parameters) {
addEzComponent(setting);
cpt++;
if (cpt % 20 == 0) addComponent(new JSeparator(JSeparator.VERTICAL));
}
}
-
+
@Override
- protected void execute()
- {
+ protected void execute() {
camera = new VideoCapture(0);
-
- for (EzVarInteger setting : parameters)
- {
+
+ for (final EzVarInteger setting : parameters) {
if (setting.getValue() == -1) continue;
-
- String propName = "CAP_PROP_" + setting.name.toUpperCase();
- try
- {
- int propID = Videoio.class.getDeclaredField(propName).getInt(null);
+
+ final String propName = "CAP_PROP_" + setting.name.toUpperCase();
+ try {
+ final int propID = Videoio.class.getDeclaredField(propName).getInt(null);
camera.set(propID, setting.getValue());
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(setting.getVariable(), e.getMessage());
}
}
-
+
// Read the first image to initialize the meta-data
- Mat mat = new Mat();
+ final Mat mat = new Mat();
camera.read(mat);
- IcyBufferedImage image = OpenCV.convertToIcy(mat);
-
+ final IcyBufferedImage image = OpenCV.convertToIcy(mat);
+
// Create the sequence
final Sequence s = new Sequence("Live webcam", image);
Icy.getMainInterface().addSequence(s);
-
+
// don't update the channel bounds on update
image.setAutoUpdateChannelBounds(false);
s.setAutoUpdateChannelBounds(false);
-
+
// Closing the sequence should stop the camera
final Thread thread = Thread.currentThread();
- s.addListener(new SequenceAdapter()
- {
+ s.addListener(new SequenceAdapter() {
@Override
- public void sequenceClosed(Sequence sequence)
- {
+ public void sequenceClosed(final Sequence sequence) {
s.removeListener(this);
thread.interrupt();
}
});
-
- FPSMeter fps = new FPSMeter();
-
- try
- {
- while (camera.read(mat) && !Thread.currentThread().isInterrupted())
- {
+
+ final FPSMeter fps = new FPSMeter();
+
+ try {
+ while (camera.read(mat) && !Thread.currentThread().isInterrupted()) {
OpenCV.convertToIcy(mat, image);
image.dataChanged();
fps.update();
getUI().setProgressBarMessage("Acquiring at " + fps.getFPS() + "fps");
}
}
- catch (Exception e)
- {
-
+ catch (final Exception e) {
+ IcyLogger.warn(this.getClass(), e);
}
- finally
- {
+ finally {
camera.release();
}
}
-
+
@Override
- public void clean()
- {
- for (EzVarInteger setting : parameters)
+ public void clean() {
+ for (final EzVarInteger setting : parameters)
setting.removeVarChangeListener(this);
parameters.clear();
}
-
+
@Override
- public void variableChanged(EzVar<Integer> source, Integer newValue)
- {
+ public void variableChanged(final EzVar<Integer> source, final Integer newValue) {
if (camera == null) return;
-
- String propName = "CAP_PROP_" + source.name.toUpperCase();
- try
- {
- int propID = Videoio.class.getDeclaredField(propName).getInt(null);
+
+ final String propName = "CAP_PROP_" + source.name.toUpperCase();
+ try {
+ final int propID = Videoio.class.getDeclaredField(propName).getInt(null);
camera.set(propID, newValue);
}
- catch (Exception e)
- {
+ catch (final Exception e) {
throw new VarException(source.getVariable(), e.getMessage());
}
}
-
+
}
diff --git a/src/main/resources/plugins/adufour/opencv/icon.png b/src/main/resources/plugins/adufour/opencv/icon.png
new file mode 100644
index 0000000000000000000000000000000000000000..33c18ccbabdd18ccf257a30267f4a085e64bb6f5
Binary files /dev/null and b/src/main/resources/plugins/adufour/opencv/icon.png differ