[ImageJ-devel] What do I need to add to my NetBeans ImgLib2 project to open a TIFF file
Curtis Rueden
ctrueden at wisc.edu
Fri Dec 5 11:17:20 CST 2014
Hi Michael,
> mvn claims to build everything OK
Yep, it did build successfully.
> % java -cp target/my-app-1.0-SNAPSHOT.jar com.mycompany.app.App
> Error: A JNI error has occurred, please check your installation and try
again
> Exception in thread "main" java.lang.NoClassDefFoundError: io/scif/SCIFIO
Maven is primarily a build tool. It puts the correct JARs on your classpath
at compile time. In your case, that is scifio-0.17.1.jar and its
dependencies.
However, the way you are launching your program is not putting the required
dependencies on the classpath. You put only my-app-1.0-SNAPSHOT.jar on the
classpath, and its dependencies are missing. So of course Java cannot find
the needed classes.
The gist is: it is your responsibility to assemble the dependencies and
ensure they are on the classpath somehow when you launch your application.
There are several ways to accomplish this. Here is one generally useful way
using Maven, which does not assume you are doing anything ImageJ-related:
$ mvn dependency:copy-dependencies
$ java -cp 'target/my-app-1.0-SNAPSHOT.jar:target/dependency/*'
com.mycompany.app.App
The "copy-dependencies" goal copies all the JAR files needed by your
program into the target/dependency folder, for easy subsequent consumption.
Alternately, the "ImageJ way" of dealing with deployment is to ship all
needed dependencies in the "jars" folder of your ImageJ application. We
created a Maven goal for this too, which you can use as follows:
$ mvn -Dimagej.app.directory=/Applications/ImageJ.app
-Ddelete.other.versions=true
Which will copy your JAR and its dependencies into your ImageJ installation
at /Applications/ImageJ.app. But note that in order for this goal to work,
you must extend the pom-imagej parent (see
https://github.com/imagej/minimal-ij1-plugin for an example).
A third solution is to use the exec-maven-plugin to launch your application
directly using Maven. E.g.:
https://github.com/imagej/imagej/blob/imagej-2.0.0-rc-17/pom.xml#L255-L278
Regards,
Curtis
On Fri, Dec 5, 2014 at 11:03 AM, Michael Ellis <michael.ellis at dsuk.biz>
wrote:
> Curtis,
>
> Thanks but it is still not working.
>
> I have cut out using NetBeans and am now just using the CLI and a text
> editor.
>
> POM as follows:
>
> ========================================================
> <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="
> http://www.w3.org/2001/XMLSchema-instance"
> xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
> http://maven.apache.org/xsd/maven-4.0.0.xsd">
> <modelVersion>4.0.0</modelVersion>
>
> <groupId>com.mycompany.app</groupId>
> <artifactId>my-app</artifactId>
> <version>1.0-SNAPSHOT</version>
> <packaging>jar</packaging>
>
> <name>my-app</name>
> <url>http://maven.apache.org</url>
>
> <properties>
> <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
> </properties>
>
> <repositories>
> <repository>
> <id>imagej.public</id>
> <url>http://maven.imagej.net/content/groups/public</url>
> </repository>
> </repositories>
>
> <dependencies>
> <dependency>
> <groupId>junit</groupId>
> <artifactId>junit</artifactId>
> <version>3.8.1</version>
> <scope>test</scope>
> </dependency>
>
> <dependency>
> <groupId>io.scif</groupId>
> <artifactId>scifio</artifactId>
> <version>0.17.1</version>
> </dependency>
>
> </dependencies>
> </project>
> ========================================================
>
> File hierarchy:
>
> .
> ./.DS_Store
> ./pom.xml
> ./src
> ./src/main
> ./src/main/java
> ./src/main/java/com
> ./src/main/java/com/mycompany
> ./src/main/java/com/mycompany/app
> ./src/main/java/com/mycompany/app/App.java
> ./src/test
> ./src/test/java
> ./src/test/java/com
> ./src/test/java/com/mycompany
> ./src/test/java/com/mycompany/app
> ./src/test/java/com/mycompany/app/AppTest.java
> ========================================================
>
> App.java as follows:
>
> package com.mycompany.app;
>
> import io.scif.FormatException;
> import io.scif.ImageMetadata;
> import io.scif.Plane;
> import io.scif.Reader;
> import io.scif.SCIFIO;
>
> public class App
> {
> public static void main( String[] args )
> {
> try {
> System.out.println( "Hello World!" );
> SCIFIO scifio = new SCIFIO();
> String sampleImage
> =
> "8bit-signed&pixelType=int8&lengths=50,50,3,5,7&axes=X,Y,Z,Channel,Time.fake";
> final Reader reader = scifio.initializer().initializeReader(sampleImage);
> System.out.printf("reader=%s%n", reader );
> } catch (Exception e) {
> System.out.printf("Exception: %s%n", e.getMessage() );
> }
> }
> }
>
> ========================================================
>
> mvm -U install
>
> [Michaels-Retina:~/temp/deleteme/my-app] michaelellis% mvn -U install
> [INFO] Scanning for projects...
> [INFO]
>
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Building my-app 1.0-SNAPSHOT
> [INFO]
> ------------------------------------------------------------------------
> [INFO]
> [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @
> my-app ---
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] skip non existing resourceDirectory
> /Users/michaelellis/temp/deleteme/my-app/src/main/resources
> [INFO]
> [INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ my-app ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 1 source file to
> /Users/michaelellis/temp/deleteme/my-app/target/classes
> [INFO]
> [INFO] --- maven-resources-plugin:2.6:testResources
> (default-testResources) @ my-app ---
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] skip non existing resourceDirectory
> /Users/michaelellis/temp/deleteme/my-app/src/test/resources
> [INFO]
> [INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @
> my-app ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 1 source file to
> /Users/michaelellis/temp/deleteme/my-app/target/test-classes
> [INFO]
> [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ my-app ---
> [INFO] Surefire report directory:
> /Users/michaelellis/temp/deleteme/my-app/target/surefire-reports
>
> -------------------------------------------------------
> T E S T S
> -------------------------------------------------------
> Running com.mycompany.app.AppTest
> Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec
>
> Results :
>
> Tests run: 1, Failures: 0, Errors: 0, Skipped: 0
>
> [INFO]
> [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ my-app ---
> [INFO] Building jar:
> /Users/michaelellis/temp/deleteme/my-app/target/my-app-1.0-SNAPSHOT.jar
> [INFO]
> [INFO] --- maven-install-plugin:2.4:install (default-install) @ my-app ---
> [INFO] Installing
> /Users/michaelellis/temp/deleteme/my-app/target/my-app-1.0-SNAPSHOT.jar to
> /Users/michaelellis/.m2/repository/com/mycompany/app/my-app/1.0-SNAPSHOT/my-app-1.0-SNAPSHOT.jar
> [INFO] Installing /Users/michaelellis/temp/deleteme/my-app/pom.xml to
> /Users/michaelellis/.m2/repository/com/mycompany/app/my-app/1.0-SNAPSHOT/my-app-1.0-SNAPSHOT.pom
> [INFO]
> ------------------------------------------------------------------------
> [INFO] BUILD SUCCESS
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Total time: 1.962 s
> [INFO] Finished at: 2014-12-05T16:59:50+00:00
> [INFO] Final Memory: 18M/242M
> [INFO] ————————————————————————————————————
>
> ========================================================
>
> mvn claims to build everything OK there seems to be no inclusion of any
> scif libraries or class files.
>
>
> When I run it I get:
>
> [Michaels-Retina:~/temp/deleteme/my-app] michaelellis% java -cp
> target/my-app-1.0-SNAPSHOT.jar com.mycompany.app.App
> Error: A JNI error has occurred, please check your installation and try
> again
> Exception in thread "main" java.lang.NoClassDefFoundError: io/scif/SCIFIO
> at java.lang.Class.getDeclaredMethods0(Native Method)
> at java.lang.Class.privateGetDeclaredMethods(Class.java:2699)
> at java.lang.Class.privateGetMethodRecursive(Class.java:3046)
> at java.lang.Class.getMethod0(Class.java:3016)
> at java.lang.Class.getMethod(Class.java:1782)
> at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
> at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
> Caused by: java.lang.ClassNotFoundException: io.scif.SCIFIO
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> ... 7 more
>
>
> ========================================================
>
> I’ve been banging my head against this for two days now.
>
> So any help appreciated
>
>
> On 5 Dec 2014, at 16:35, Curtis Rueden <ctrueden at WISC.EDU> wrote:
>
> Hi Michael,
>
> > The POM for io.scif:scifio:jar:0.17.1 is missing, no dependency
> > information available
>
> Make sure you have the following <repositories> block in your POM:
>
> <repositories>
> <repository>
> <id>imagej.public</id>
> <url>http://maven.imagej.net/content/groups/public</url>
> </repository>
> </repositories>
>
> Then rebuild with the "-U" flag. I don't know how to do this from
> NetBeans, but you only need to do it once from the CLI -- then you can
> return to NetBeans and it should work.
>
> Regards,
> Curtis
>
> On Fri, Dec 5, 2014 at 6:07 AM, Michael Ellis <michael.ellis at dsuk.biz>
> wrote:
>
>> I have followed the advice offered by Curtis regarding adding
>> the io.scif: scifio dependency to my POM
>>
>> The dependency part of my POM looks like this:
>>
>> <dependencies>
>> <dependency>
>> <groupId>net.imglib2</groupId>
>> <artifactId>imglib2</artifactId>
>> <version>2.2.1-SNAPSHOT</version>
>> <type>jar</type>
>> </dependency>
>> <dependency>
>> <groupId>io.scif</groupId>
>> <artifactId>scifio</artifactId>
>> <version>0.17.1</version>
>> <type>jar</type>
>> </dependency>
>> </dependencies>
>>
>> I am using NetBeans IDE, configured for use with maven project (I am slo
>> using Java 8 and JavaFX)
>>
>> However when I attempt to Build (or Build with Dependencies) within
>> NetBeans, I get the following error message:
>> ============================================================
>>
>> cd /Users/michaelellis/Documents/Development/MavenImgLib2FX;
>> JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_40.jdk/Contents/Home
>> "/Applications/NetBeans/NetBeans
>> 8.0.app/Contents/Resources/NetBeans/java/maven/bin/mvn" install
>> Scanning for projects...
>>
>> ------------------------------------------------------------------------
>> Building MavenImgLib2FX 1.0-SNAPSHOT
>> ------------------------------------------------------------------------
>> The POM for io.scif:scifio:jar:0.17.1 is missing, no dependency
>> information available
>> ------------------------------------------------------------------------
>> BUILD FAILURE
>> ------------------------------------------------------------------------
>> Total time: 0.341s
>> Finished at: Fri Dec 05 10:34:41 GMT 2014
>> Final Memory: 7M/245M
>> ------------------------------------------------------------------------
>> Failed to execute goal on project MavenImgLib2FX: Could not resolve
>> dependencies for project biz.dsuk:MavenImgLib2FX:jar:1.0-SNAPSHOT: Failure
>> to find io.scif:scifio:jar:0.17.1 in http://repo.maven.apache.org/maven2
>> was cached in the local repository, resolution will not be reattempted
>> until the update interval of central has elapsed or updates are forced ->
>> [Help 1]
>>
>> To see the full stack trace of the errors, re-run Maven with the -e
>> switch.
>> Re-run Maven using the -X switch to enable full debug logging.
>>
>> For more information about the errors and possible solutions, please read
>> the following articles:
>> [Help 1]
>> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
>>
>> ============================================================
>>
>> If I open a terminal window and cd into the project directory and:
>>
>> mvn clean package
>>
>> It succeeds.
>>
>> However, when I then attempt to run the project with:
>>
>> java -cp MavenImgLib2FX-1.0-SNAPSHOT.jar biz.dsuk.mavenimglib2fx.MainApp
>>
>> The application starts to execute but throws “No compatible service:
>> io.scif.SCIFIOService” exception.
>> ============================================================
>>
>> img1=CellImg [20x30]
>> BufferedImage=BufferedImage at 3137c585: type = 10 ColorModel: #pixelBits =
>> 8 numComponents = 1 color space = java.awt.color.ICC_ColorSpace at 134d9d5f
>> transparency = 1 has alpha = false isAlphaPre = false
>> ByteInterleavedRaster: width = 707 height = 699 #numDataElements 1
>> dataOff[0] = 0
>> Loading image...
>> Exception in Application start method
>> java.lang.reflect.InvocationTargetException
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> at java.lang.reflect.Method.invoke(Method.java:497)
>> at
>> com.sun.javafx.application.LauncherImpl.launchApplicationWithArgs(LauncherImpl.java:363)
>> at
>> com.sun.javafx.application.LauncherImpl.launchApplication(LauncherImpl.java:303)
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> at java.lang.reflect.Method.invoke(Method.java:497)
>> at sun.launcher.LauncherHelper$FXHelper.main(LauncherHelper.java:767)
>> Caused by: java.lang.RuntimeException: Exception in Application start
>> method
>> at
>> com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:875)
>> at
>> com.sun.javafx.application.LauncherImpl.lambda$launchApplication$150(LauncherImpl.java:157)
>> at
>> com.sun.javafx.application.LauncherImpl$$Lambda$50/553264065.run(Unknown
>> Source)
>> at java.lang.Thread.run(Thread.java:745)
>> Caused by: java.lang.IllegalArgumentException: No compatible service:
>> io.scif.SCIFIOService
>> at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:243)
>> at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
>> at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:170)
>> at org.scijava.Context.<init>(Context.java:244)
>> at org.scijava.Context.<init>(Context.java:203)
>> at org.scijava.Context.<init>(Context.java:142)
>> at org.scijava.Context.<init>(Context.java:128)
>> at io.scif.SCIFIO.<init>(SCIFIO.java:81)
>> at biz.dsuk.mavenimglib2fx.MainApp.start(MainApp.java:38)
>> at
>> com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$156(LauncherImpl.java:821)
>> at
>> com.sun.javafx.application.LauncherImpl$$Lambda$53/681110827.run(Unknown
>> Source)
>> at
>> com.sun.javafx.application.PlatformImpl.lambda$runAndWait$169(PlatformImpl.java:326)
>> at
>> com.sun.javafx.application.PlatformImpl$$Lambda$47/693632176.run(Unknown
>> Source)
>> at
>> com.sun.javafx.application.PlatformImpl.lambda$null$167(PlatformImpl.java:295)
>> at
>> com.sun.javafx.application.PlatformImpl$$Lambda$49/1260282780.run(Unknown
>> Source)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at
>> com.sun.javafx.application.PlatformImpl.lambda$runLater$168(PlatformImpl.java:294)
>> at
>> com.sun.javafx.application.PlatformImpl$$Lambda$48/1364335809.run(Unknown
>> Source)
>> at
>> com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95)
>> Exception running application biz.dsuk.mavenimglib2fx.MainApp
>> ============================================================
>>
>> If I remove the calls to the SCIO code and build and run from the command
>> line, all works well.
>>
>> The SCIO source code that I am using is lifted/amended from one of the
>> tutorials and is as follows:
>>
>> ============================================================
>> imagePath =
>> "8bit-signed&pixelType=int8&lengths=50,50,3,5,7&axes=X,Y,Z,Channel,Time.fake";
>> System.out.println("Loading image... '" + imagePath + "'");
>> SCIFIO scifio = new SCIFIO();
>> final Reader reader =
>> scifio.initializer().initializeReader(imagePath);
>> ============================================================
>>
>> This source code works file in the SCIFIO tutorial.
>>
>> Any help gratefully appreciated!!!!!
>>
>> — Michael Ellis
>>
>>
>>
>>
>> On 3 Dec 2014, at 19:31, Curtis Rueden <ctrueden at WISC.EDU> wrote:
>>
>> Hi Michael,
>>
>> > How do I establish what Maven projects I need to include?
>>
>> One way to check is using the dependency-maven-plugin like so:
>>
>> mvn dependency:analyze
>>
>> This will tell you:
>>
>> A) Dependencies you declared but do not actually use; and
>> B) Dependencies you did not declare directly, but actually need.
>>
>> Note that this will only work if your project compiles successfully. In
>> other words, it is easier to start with "too many" dependencies and pare
>> down, rather than trying to "build up" from zero.
>>
>> So in your case, you can start with the ImgLib2 Examples dependencies
>> block, run dependency:analyze, and adjust the POM according to its
>> recommendations.
>>
>> > When I go to my NetBeans project dependence, select Add dependency,
>> > then type SCIF to the query text box, I get a huge list of
>> > possibilities.
>>
>> The dependency you probably want is io.scif:scifio (i.e.: a groupId of
>> io.scif, and an artifactId of scifio). Presumably at the latest version.
>> You can search for that here:
>>
>> http://maven.imagej.net/index.html#nexus-search;gav~io.scif~scifio~~~
>>
>> So your dependency block in this case would be:
>>
>> <dependency>
>> <groupId>io.scif</groupId>
>> <artifactId>scifio</artifactId>
>> <version>0.17.1</version>
>> </dependency>
>>
>> Note that that block of XML is available for copy-pasting from the link
>> above.
>>
>> > I am completely new to maven
>>
>> For more information, see:
>> http://imagej.net/Maven
>>
>> Regards,
>> Curtis
>>
>> On Tue, Dec 2, 2014 at 6:05 PM, Michael Ellis <michael.ellis at dsuk.biz>
>> wrote:
>>
>>> I am investigating the using ImgLib2 for a project.
>>>
>>> I am using NetBeans and have managed to create a NetBeans Mavern project
>>> and have added a dependency for ImgLib2 Core Library and that seems to be
>>> working OK.
>>>
>>> I now want to add the least possible requirements for the purpose of
>>> opening some image files.
>>>
>>> How do I establish what Maven projects I need to include?
>>>
>>> I have cloned the ImgLib2 Examples project and got that working but
>>> that seems to include all manner of things that I suspect I do not need.
>>>
>>> When I go to my NetBeans project dependence, select Add dependency, then
>>> type SCIF to the query text box, I get a huge list of possibilities.
>>>
>>> I am completely new to maven and so do not know what I am doing with it!
>>>
>>> — Michael Ellis
>>> Digital Scientific UK Ltd.
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> ImageJ-devel mailing list
>>> ImageJ-devel at imagej.net
>>> http://imagej.net/mailman/listinfo/imagej-devel
>>>
>>>
>>
>>
>> _______________________________________________
>> ImageJ-devel mailing list
>> ImageJ-devel at imagej.net
>> http://imagej.net/mailman/listinfo/imagej-devel
>>
>>
>
>
> _______________________________________________
> ImageJ-devel mailing list
> ImageJ-devel at imagej.net
> http://imagej.net/mailman/listinfo/imagej-devel
>
>
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