Dear Curtis,
Thank you for your reply. It will be a couple of days before I am working on
this again but thanks for the pointers.
— Michael Ellis
On 18 Dec 2014, at 22:28, Curtis Rueden <ctrue...@wisc.edu> wrote:
> Hi Michael,
>
> > The Example6c has not been updated to reflect the new way of doing
> > things.
>
> Indeed. If you end up updating it, a pull request to that effect would be
> most welcome!
>
> > You previously pointed me at the ImageJ OPS library. Is that th best
> > way of achieving the convolution?
>
> The most future-proof, in that OPS is the direction we are going. However, at
> this point in time it won't be the smoothest ride, since the OPS library is
> still in incubation.
>
> Furthermore, the main OPS convolve routine leans on the ImgLib2
> FFTConvolution implementation, so if all you need is the low-level function,
> then OPS is probably not necessary for you.
>
> > [INFO] Restricted to JDK 1.6 yet com.sun:tools:jar:1.4.2:system
> > contains com/sun/codemodel/internal/ClassType.class targeted to JDK
> > 1.8
>
> This was a bug in the Maven build configuration, addressed earlier this week.
> Should work with the latest master.
>
> > So what are the minimal hoops I need to jump though to setup ops such
> > that the code below will compile? (I want to avoid dragging in any
> > ImageJ 1 legacy code)
> >
> > Img<FloatType> result = image.copy();
> > Op op = ops.op("convolve", result, image, templateInverse);
>
> OPS does not depend on ImageJ1. (The only ImageJ2 component that does is
> called imagej-legacy, and is expressly for the purpose of backwards
> compatibility.)
>
> Easiest would be to start with the "using-ops" tutorial project, and edit the
> code from there.
>
> https://github.com/imagej/imagej-tutorials/tree/31a5771277682e5f1ef45112094d147539dc4bc7/using-ops
>
> FTR, you can invoke the routine with something like:
>
> Object result = ops.convolve(image, templateInverse);
>
> However, in attempting a quick test of the convolve routine, I ran into some
> obstacles with the current code. My advice at the moment is to just use
> FFTConvolution directly for your needs.
>
> > For the record, I am suspicious about Java annotations!
>
> I agree with your concerns: they do unfortunately obfuscate the execution
> flow. However, they also bring many advantages. In particular, the way we are
> using them provides: 1) a dependency injection mechanism without the need for
> any external configuration files; and 2) a very succinct syntax for
> parameterized commands. We are shooting for DRY ("Don't Repeat Yourself")
> code here [1], not just in the core, but particularly for plugin developers
> [2].
>
> I think the best way to counter the mystery surrounding the inner workings is
> to thoroughly document how things work.
>
> Regards,
> Curtis
>
> P.S. Related to FFTConvolution, see also these issues:
> * https://github.com/imglib/imglib2-algorithm-fft/pull/1
> * https://github.com/imglib/imglib2/issues/61
> * https://github.com/imagej/imagej-ops/issues/12
>
> [1] http://imagej.net/Philosophy#Convention_over_configuration
> [2] Example:
> http://curtis.imagej.net/2013-03-15-imagej-research-paper/plugin-comparison.png
>
> On Wed, Dec 10, 2014 at 1:09 PM, Michael Ellis <michael.el...@dsuk.biz> wrote:
> Curtis,
>
> Thanks for this reply and I am now turning my attention to use of the FFT.
>
> It seems the FFT was moved from imglib2-algorithm to imglib2-algorithm-fft
> (due I think to licensing issues).
>
> I need to achieve what is done in imglib2-tutorials/Example6c.java at master
> · imglib/imglib2-tutorials
>
> The Example6c has not been updated to reflect the new way of doing things. If
> I clone the imglib/imglib2-tutorials project I see the following are all
> deprecated.
>
> import net.imglib2.algorithm.fft.FourierConvolution;
> import net.imglib2.algorithm.fft.FourierTransform;
> import net.imglib2.algorithm.fft.InverseFourierTransform;
>
> I have managed to make progress and think I have got fourier and inverse
> fourier transforms working. So that just leaves the convolution.
>
> You previously pointed me at the ImageJ OPS library. Is that th best way of
> achieving the convolution?
>
> The ImageJ OPS example however depends on ImageJ. The ImageJ OPS test
> programs don’t help me either since the test classes do some magic wizardry
> that I do not understand at all i.e. with Contexts, Java annotations and some
> injection stuff.
>
> So what are the minimal hoops I need to jump though to setup ops such that
> the code below will compile? (I want to avoid dragging in any ImageJ 1 legacy
> code)
>
> Img<FloatType> result = image.copy();
> Op op = ops.op("convolve", result, image, templateInverse);
>
> Also in downloading the ImageJ-Ops project and running maven compile, I get
> the following. I realise that I am at Java8 and that might be jumping the gun
> a bit, but Java 6 is well past its sell by date and if you are on a new Apple
> Mac, Java 6 is not a comfortable option.
>
> [INFO] Restricted to JDK 1.6 yet com.sun:tools:jar:1.4.2:system contains
> com/sun/codemodel/internal/ClassType.class targeted to JDK 1.8
> [WARNING] Rule 1: org.apache.maven.plugins.enforcer.EnforceBytecodeVersion
> failed with message:
> Found Banned Dependency: com.sun:tools:jar:1.4.2
>
> For the record, I am suspicious about Java annotations! *For me at least*
> They fro not help with trying to understand code as I cannot make out how to
> call the code in question. The feel rather like something layered on top of a
> language rather than an intrinsic built in. They give me that uncomfortable
> feeling that C++ Standard Template Library did - and that gave me nightmares
> when it came time to debug code.
>
> Thanks in anticipation of any light you can throw into my darkness!
>
> — Michael Ellis
>
>
>
>
>
>
>
> On 5 Dec 2014, at 18:31, Curtis Rueden <ctrue...@wisc.edu> wrote:
>
>> Hi Michael,
>>
>> > It looks like there is a new FFT but the tutorials use the older
>> > version.
>> >
>> > What should I go with?
>>
>> The library for doing FFT is imglib2-algorithm-fft:
>> https://github.com/imglib/imglib2-algorithm-fft
>>
>> Regarding the "new FFT", perhaps you refer to this?
>> https://github.com/imglib/imglib2-algorithm-fft/pull/1
>>
>> At the moment there are licensing issues with imglib2-algorithm-fft (it
>> depends on the Mines JTK library which has a license incompatible with GPL).
>> That PR addresses the issues by using the JTransforms library instead.
>>
>> You also might want to consider using the higher level ImageJ OPS library:
>> https://github.com/imagej/imagej-ops
>>
>> Thanks to the efforts of Brian Northan, we are about to merge an OP wrapper
>> for FFT:
>> https://github.com/imagej/imagej-ops/pull/76
>>
>> Note that these components are still in the 0.x incubation phase, meaning
>> they do not have stable APIs. That said, we would really appreciate early
>> adopters who can try out the code and help drive things in the right
>> direction.
>>
>> We will be reviewing and merging these improvements over the next few days,
>> then cutting new releases of imglib2-algorithm-fft and imagej-ops. At that
>> point, it should be easier for you to try them out.
>>
>> The relevant tutorials are based on imglib2-algorithm-fft:
>>
>> https://github.com/imglib/imglib2-tutorials/blob/929de9b7482c312ff9c51ab52aa632779ef058f3/src/main/java/Example6b.java
>>
>> https://github.com/imglib/imglib2-tutorials/blob/929de9b7482c312ff9c51ab52aa632779ef058f3/src/main/java/Example6c.java
>>
>> And IIUC the changes above are internal so the tutorial code should not
>> requiring updating (beyond an update to the version of imglib2-algorithm-fft
>> in the POM, of course).
>>
>> Regards,
>> Curtis
>>
>> On Fri, Dec 5, 2014 at 12:21 PM, Michael Ellis <michael.el...@dsuk.biz>
>> wrote:
>> Once again, Curtis
>>
>> I really appreciate your help with this.
>>
>> Next questions on the horizon will involve the ImgLib2 algorithm FFT
>> classes. It looks like there is a new FFT but the tutorials use the older
>> version.
>>
>> What should I go with?
>>
>> My aim is build an application, which as part of it will be doing image
>> alignment using FFT phase correlation.
>>
>> Regards — Michael Ellis
>>
>>
>> On 5 Dec 2014, at 18:13, Curtis Rueden <ctrue...@wisc.edu> wrote:
>>
>>> Hi Michael,
>>>
>>> > gives me a self contained runnable jar. Progress! I’m learning.
>>> >
>>> > BUT as before when I run the jar, I get the Exception: No compatible
>>> > service: org.scijava.service.SciJavaService
>>>
>>> Self contained runnable JARs (i.e., uber-jars) are convenient in some ways,
>>> but come with a host of problems.
>>>
>>> 1) If you do not shade your dependencies (i.e., rename their packages),
>>> then you may ship duplicate and/or incompatible classes with other
>>> libraries. This makes your library much harder to reuse in a shared system
>>> such as an ImageJ installation.
>>>
>>> 2) You cannot ship piecemeal updates to individual dependencies -- i.e.,
>>> every time your code changes, you must ship a new (possibly very large) new
>>> JAR file to your users.
>>>
>>> 3) The SciJava annotation processor, responsible for indexing the @Plugin
>>> annotations that drive SciJava/ImageJ2/etc. plugins, writes the metadata
>>> into a resource file at META-INF/json/org.scijava.plugin.Plugin within the
>>> JAR. If you try to create an uber-jar via the assembly or shade plugin, the
>>> default combination algorithm will overwrite those files, stomping the
>>> annotations.
>>>
>>> We wrote some code which offers one way around this:
>>>
>>> https://github.com/imagej/imagej/blob/imagej-2.0.0-rc-17/pom.xml#L614-L631
>>>
>>> For more on uber-jars, see also:
>>>
>>> http://imagej.net/Frequently_Asked_Questions#How_can_I_call_ImageJ_from_my_software.3F
>>>
>>> The gist is: avoid using an uber-jar unless you really need it.
>>>
>>> > I’ve got it working with your help!
>>>
>>> Awesome, congratulations. Let us know if you encounter any more roadblocks.
>>>
>>> Regards,
>>> Curtis
>>>
>>> On Fri, Dec 5, 2014 at 12:03 PM, Michael Ellis <michael.el...@dsuk.biz>
>>> wrote:
>>> Adding a build section to the POM:
>>>
>>> <build>
>>> <plugins>
>>> <plugin>
>>> <groupId>org.apache.maven.plugins</groupId>
>>> <artifactId>maven-shade-plugin</artifactId>
>>> <version>2.3</version>
>>> <executions>
>>> <execution>
>>> <phase>package</phase>
>>> <goals>
>>> <goal>shade</goal>
>>> </goals>
>>> <configuration>
>>> <transformers>
>>> <transformer
>>> implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
>>> <manifestEntries>
>>> <Main-Class>com.mycompany.app.App</Main-Class>
>>> <Build-Number>123</Build-Number>
>>> </manifestEntries>
>>> </transformer>
>>> </transformers>
>>> </configuration>
>>> </execution>
>>> </executions>
>>> </plugin>
>>> </plugins>
>>> </build>
>>>
>>> To the POM gives me a self contained runnable jar. Progress! I’m learning.
>>>
>>> BUT as before when I run the jar, I get the Exception: No compatible
>>> service: org.scijava.service.SciJavaService
>>> =================================================================
>>>
>>> [Michaels-Retina:~/temp/deleteme/my-app] michaelellis% java -jar
>>> target/my-app-1.0-SNAPSHOT.jar
>>> Hello World!
>>> Exception: No compatible service: org.scijava.service.SciJavaService
>>> =================================================================
>>>
>>> Still vexed!
>>>
>>>
>>> On 5 Dec 2014, at 17:17, Curtis Rueden <ctrue...@wisc.edu> wrote:
>>>
>>>> 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.el...@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 <ctrue...@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.el...@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@3137c585: type = 10 ColorModel: #pixelBits =
>>>>> 8 numComponents = 1 color space = java.awt.color.ICC_ColorSpace@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 <ctrue...@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.el...@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@imagej.net
>>>>>> http://imagej.net/mailman/listinfo/imagej-devel
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> ImageJ-devel mailing list
>>>>> ImageJ-devel@imagej.net
>>>>> http://imagej.net/mailman/listinfo/imagej-devel
>>>>>
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> ImageJ-devel mailing list
>>>> ImageJ-devel@imagej.net
>>>> http://imagej.net/mailman/listinfo/imagej-devel
>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> ImageJ-devel mailing list
>>> ImageJ-devel@imagej.net
>>> http://imagej.net/mailman/listinfo/imagej-devel
>>>
>>>
>>
>>
>
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