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‎.settings/org.eclipse.jdt.core.prefs‎

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@@ -9,6 +9,7 @@ org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nul
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org.eclipse.jdt.core.compiler.annotation.nullable.secondary=
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org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled
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org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
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org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
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org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
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org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
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org.eclipse.jdt.core.compiler.compliance=1.8

‎pom.xml‎

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@@ -110,16 +110,118 @@
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</repositories>
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<dependencies>
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<dependency>
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<groupId>net.preibisch</groupId>
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<artifactId>imagej-clustering</artifactId>
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<version>0.2.1-SNAPSHOT</version><!--
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<version>${imagej-clustering.version}</version> -->
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<groupId>net.imagej</groupId>
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<artifactId>imagej</artifactId>
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</dependency>
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<dependency>
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<groupId>net.imagej</groupId>
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<artifactId>imagej-legacy</artifactId>
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</dependency>
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<dependency>
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<groupId>net.imglib2</groupId>
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<artifactId>imglib2</artifactId>
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</dependency>
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<dependency>
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<groupId>net.imagej</groupId>
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<artifactId>ij</artifactId>
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</dependency>
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<dependency>
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<groupId>net.imglib2</groupId>
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<artifactId>imglib2-ij</artifactId>
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</dependency>
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<!-- <dependency> <groupId>net.imglib2</groupId> <artifactId>imglib2-ui</artifactId>
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</dependency> <dependency> <groupId>net.imglib2</groupId> <artifactId>imglib2-realtransform</artifactId>
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</dependency> <dependency> <groupId>net.imglib2</groupId> <artifactId>imglib2-algorithm</artifactId>
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</dependency> -->
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<dependency>
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<groupId>sc.fiji</groupId>
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<artifactId>bigdataviewer-core</artifactId>
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</dependency>
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<dependency>
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<groupId>sc.fiji</groupId>
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<artifactId>Fiji_Plugins</artifactId>
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</dependency>
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<dependency>
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<groupId>io.scif</groupId>
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<artifactId>scifio</artifactId>
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</dependency>
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<dependency>
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<groupId>io.scif</groupId>
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<artifactId>scifio-bf-compat</artifactId>
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<scope>runtime</scope>
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</dependency>
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<!-- The formats-bsd component adds support for open formats. -->
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<dependency>
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<groupId>ome</groupId>
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<artifactId>formats-bsd</artifactId>
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<scope>runtime</scope>
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</dependency>
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<!-- The formats-gpl component adds support for proprietary formats. -->
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<dependency>
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<groupId>ome</groupId>
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<artifactId>formats-gpl</artifactId>
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<scope>runtime</scope>
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</dependency>
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<!-- https://mvnrepository.com/artifact/com.jcraft/jsch -->
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<dependency>
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<groupId>com.jcraft</groupId>
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<artifactId>jsch</artifactId>
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<version>0.1.54</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/com.google.guava/guava -->
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<dependency>
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<groupId>com.google.guava</groupId>
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<artifactId>guava</artifactId>
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<version>r05</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/org.apache.kafka/kafka -->
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<dependency>
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<groupId>commons-io</groupId>
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<artifactId>commons-io</artifactId>
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<version>2.4</version>
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</dependency>
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<!-- https://mvnrepository.com/artifact/com.google.code.gson/gson -->
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<dependency>
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<groupId>com.google.code.gson</groupId>
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<artifactId>gson</artifactId>
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<version>2.8.5</version>
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</dependency>
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<dependency>
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<groupId>net.preibisch</groupId>
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<artifactId>multiview-reconstruction</artifactId>
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<version>0.2.17</version>
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</dependency>
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<dependency>
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<groupId>org.janelia.saalfeldlab</groupId>
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<artifactId>n5-imglib2</artifactId>
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<version>3.4.0</version>
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</dependency>
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<dependency>
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<groupId>org.apache.kafka</groupId>
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<artifactId>kafka_2.12</artifactId>
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<version>1.1.0</version>
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</dependency>
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<!-- <dependency> <groupId>ome</groupId> <artifactId>bio-formats_plugins</artifactId>
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</dependency> -->
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<dependency>
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<groupId>info.picocli</groupId>
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<artifactId>picocli</artifactId>
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<version>3.9.2</version>
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</dependency>
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<dependency>
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<groupId>net.preibisch</groupId>
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<artifactId>imagej-clustering</artifactId>
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<version>0.2.1-SNAPSHOT</version><!-- <version>${imagej-clustering.version}</version> -->
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</dependency>
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</dependencies>
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<build>
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<sourceDirectory>${basedir}/src/net/preibisch</sourceDirectory>
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<plugins>
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<!-- download source code in Eclipse, best practice -->
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</descriptorRefs>
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<!-- MainClass in mainfest make a executable jar -->
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<archive>
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<manifest>
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<mainClass>net.preibisch.fusiontask.task.MainJob</mainClass>
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</manifest>
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<manifest>
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<mainClass>net.preibisch.fusiontask.task.MainJob</mainClass>
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</manifest>
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</archive>
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</configuration>
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<executions>
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<execution>
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<id>make-assembly</id>
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<!-- bind to the packaging phase -->
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<phase>package</phase>
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<goals>
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<goal>single</goal>
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</goals>
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</execution>
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<execution>
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<id>make-assembly</id>
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<!-- bind to the packaging phase -->
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<phase>package</phase>
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<goals>
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<goal>single</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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</plugins>
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<!-- <plugins>
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<plugin>
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<artifactId>maven-assembly-plugin</artifactId>
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<configuration>
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<archive>
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<manifest>
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<mainClass>main.java.net.preibisch.fusiontask.task.MainJob</mainClass>
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</manifest>
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</archive>
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<descriptorRefs>
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<descriptorRef>jar-with-dependencies</descriptorRef>
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</descriptorRefs>
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</configuration>
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</plugin>
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</plugins> -->
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<!-- <plugins> <plugin> <artifactId>maven-assembly-plugin</artifactId>
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<configuration> <archive> <manifest> <mainClass>main.java.net.preibisch.fusiontask.task.MainJob</mainClass>
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</manifest> </archive> <descriptorRefs> <descriptorRef>jar-with-dependencies</descriptorRef>
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</descriptorRefs> </configuration> </plugin> </plugins> -->
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</build>
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</project>

‎src/net/preibisch/fusiontask/task/MainJob.java‎

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Original file line numberDiff line numberDiff line change
@@ -130,8 +130,8 @@ public static void generateN5fromXML(String inputPath, String metadataPath, Stri
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public static void main(String[] args) {
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// new ImageJ();
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// String str = "-t proc -i /Users/Marwan/Desktop/Task/grid-3d-stitched-h5/dataset.xml -o /Users/Marwan/Desktop/Task/output.n5 -m /Users/Marwan/Desktop/Task/metadata.json -id 1";
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System.out.println(String.join(" ", args));
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CommandLine.call(new MainJob(), args);
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String str = "-t proc -i /Users/Marwan/Desktop/Task/grid-3d-stitched-h5/dataset.xml -o /Users/Marwan/Desktop/Task/output.n5 -m /Users/Marwan/Desktop/Task/metadata.json -id 1";
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// System.out.println(String.join(" ", args));
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CommandLine.call(new MainJob(), str.split(" "));
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}
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}

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