[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 10:35:23 CST 2014
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
>>
>>
>
>
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> http://imagej.net/mailman/listinfo/imagej-devel
>
>
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