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imagej / imagej2

Open scientific N-dimensional image processing :microscope: :sparkler:
https://imagej.net/
BSD 2-Clause "Simplified" License
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Fresh downloaded Fiji does not startup on Windows7 x64 #160

Closed haesleinhuepf closed 6 years ago

haesleinhuepf commented 7 years ago

Hey guys,

I just downloaded a fresh Fiji. When starting it, it closes after some seconds. When running it as debug.exe, it says 

[DEBUG] Created service 'org.scijava.app.DefaultAppService' in 2 ms
[DEBUG] Creating service: org.scijava.parse.DefaultParseService
[DEBUG] Created service 'org.scijava.parse.DefaultParseService' in 1 ms
[DEBUG] Created service 'org.scijava.script.DefaultScriptService' in 10 ms
[DEBUG] Creating service: org.scijava.app.DefaultStatusService
[DEBUG] Created service 'org.scijava.app.DefaultStatusService' in 1 ms
[DEBUG] Creating service: io.scif.services.SCIFIODatasetService
[DEBUG] Created service 'io.scif.services.SCIFIODatasetService' in 6 ms
[DEBUG] Creating service: org.scijava.display.DefaultDisplayService
[DEBUG] Created service 'org.scijava.display.DefaultDisplayService' in 3 ms
[DEBUG] Creating service: org.scijava.menu.DefaultMenuService
[DEBUG] Created service 'org.scijava.menu.DefaultMenuService' in 2 ms
[DEBUG] Creating service: net.imagej.display.DefaultOverlayService
[DEBUG] Creating service: net.imagej.ui.awt.AWTRenderingService
[DEBUG] Created service 'net.imagej.ui.awt.AWTRenderingService' in 1 ms
[DEBUG] Created service 'net.imagej.display.DefaultOverlayService' in 7 ms
[DEBUG] Creating service: net.imagej.threshold.DefaultThresholdService
[DEBUG] Created service 'net.imagej.threshold.DefaultThresholdService' in 3 ms
[DEBUG] Found 6 App plugins.
[DEBUG] Found 10 ScriptLanguage plugins.
[DEBUG] Not overwriting name 'Clojure':
        proposed = org.scijava.plugins.scripting.clojure.ClojureScriptLanguage
        existing = org.scijava.plugins.scripting.clojure.ClojureScriptLanguage
[DEBUG] Not overwriting name 'Java':
        proposed = org.scijava.plugins.scripting.java.JavaScriptLanguage
        existing = org.scijava.plugins.scripting.java.JavaScriptLanguage
[DEBUG] Not overwriting name 'JavaScript':
        proposed = org.scijava.plugins.scripting.javascript.JavaScriptScriptLang
uage
        existing = org.scijava.plugins.scripting.javascript.JavaScriptScriptLang
uage
[DEBUG] Ignoring unsupported script: trackmateGraph.m
[DEBUG] Ignoring unsupported script: Miji.m
[DEBUG] Ignoring unsupported script: trackmateSpots.m
[DEBUG] Ignoring unsupported script: Matlab3DViewerDemo_3.m
[DEBUG] Ignoring unsupported script: Matlab3DViewerDemo_2.m
[DEBUG] Ignoring unsupported script: Matlab3DViewerDemo_1.m
[DEBUG] Ignoring unsupported script: Matlab3DViewerIntroduction.m
[DEBUG] Ignoring unsupported script: copytoImg.m
[DEBUG] Ignoring unsupported script: trackmateFeatureDeclarations.m
[DEBUG] Ignoring unsupported script: ImageJ.m
[DEBUG] Ignoring unsupported script: Miji_Test.m
[DEBUG] Ignoring unsupported script: InstallJava3D.m
[DEBUG] Ignoring unsupported script: trackmateImageCalibration.m
[DEBUG] Ignoring unsupported script: copytoImgPlus.m
[DEBUG] Ignoring unsupported script: IsJava3DInstalled.m
[DEBUG] Ignoring unsupported script: trackmateEdges.m
[DEBUG] Ignoring unsupported script: importTrackMateTracks.m
[DEBUG] Ignoring unsupported script: copytoMatlab.m
[DEBUG] Ignoring unsupported script: bfopen.m
[DEBUG] Ignoring unsupported script: Series_Labeler-2.0.0.jar
[DEBUG] Ignoring unsupported script: Dichromacy_-2.1.0.jar
[DEBUG] Ignoring unsupported script: Javascript_-2.0.0-SNAPSHOT.jar
[DEBUG] Ignoring unsupported script: Cell_Counter-2.2.1.jar
[DEBUG] Ignoring unsupported script: Auto_Threshold-1.16.4.jar
[DEBUG] Ignoring unsupported script: Gray_Morphology-2.3.3.jar
[DEBUG] Ignoring unsupported script: Macros/Bulls_Eye.txt
[DEBUG] Ignoring unsupported script: TrakEM2_Archipelago-2.0.1.jar
[DEBUG] Ignoring unsupported script: Simple_Neurite_Tracer-3.0.6.jar
[DEBUG] Ignoring unsupported script: Correct_3D_Drift-1.0.0.jar
[DEBUG] Ignoring unsupported script: Fiji_Plugins-3.0.0.jar
[DEBUG] Ignoring unsupported script: CLI_-2.0.0-SNAPSHOT.jar
[DEBUG] Ignoring unsupported script: KymographBuilder-1.2.3.jar
[DEBUG] Ignoring unsupported script: QuickPALM_-1.1.1.jar
[DEBUG] Ignoring unsupported script: Colour_Deconvolution-3.0.1.jar
[DEBUG] Ignoring unsupported script: Time_Lapse-2.0.1.jar
[DEBUG] Ignoring unsupported script: Bug_Submitter-2.1.0.jar
[DEBUG] Ignoring unsupported script: blockmatching_-2.1.1.jar
[DEBUG] Ignoring unsupported script: Siox_Segmentation-1.0.4.jar
[DEBUG] Ignoring unsupported script: registration_3d-2.0.0.jar
[DEBUG] Ignoring unsupported script: Macros/Polygon_.txt
[DEBUG] Ignoring unsupported script: bUnwarpJ_-2.6.4.jar
[DEBUG] Ignoring unsupported script: H5J_Loader_Plugin-1.0.6.jar
[DEBUG] Ignoring unsupported script: Color_Histogram-2.0.6.jar
[DEBUG] Ignoring unsupported script: Differentials_-2.0.0.jar
[DEBUG] Ignoring unsupported script: Refresh_Javas-2.0.0-SNAPSHOT.jar
[DEBUG] Ignoring unsupported script: Descriptor_based_registration-2.1.1.jar
[DEBUG] Ignoring unsupported script: SheppLogan_-2.0.0.jar
[DEBUG] Ignoring unsupported script: Manual_Tracking-2.1.0.jar
[DEBUG] Ignoring unsupported script: register_virtual_stack_slices-3.0.1.jar
[DEBUG] Ignoring unsupported script: VIB_-3.0.1.jar
[DEBUG] Ignoring unsupported script: Archipelago_Plugins-0.5.2.jar
[DEBUG] Ignoring unsupported script: trakem2_tps-1.1.2.jar
[DEBUG] Ignoring unsupported script: TrakEM2_-1.0h.jar
[DEBUG] Ignoring unsupported script: panorama_-3.0.1.jar
[DEBUG] Ignoring unsupported script: View5D_-1.3.1.jar
[DEBUG] Ignoring unsupported script: Extended_Depth_Field-2.0.1.jar
[DEBUG] Ignoring unsupported script: LSM_Toolbox-4.1.1.jar
[DEBUG] Ignoring unsupported script: AnalyzeSkeleton_-3.1.1.jar
[DEBUG] Ignoring unsupported script: Fiji_Updater.jar
[DEBUG] Ignoring unsupported script: Helmholtz_Analysis-2.0.1.jar
[DEBUG] Ignoring unsupported script: IsoData_Classifier-2.0.0.jar
[DEBUG] Ignoring unsupported script: LSM_Reader-4.1.1.jar
[DEBUG] Ignoring unsupported script: BalloonSegmentation_-2.0.0.jar
[DEBUG] Ignoring unsupported script: Vaa3d_Reader-2.0.1.jar
[DEBUG] Ignoring unsupported script: Graph_Cut-1.0.1.jar
[DEBUG] Ignoring unsupported script: bigdataviewer_fiji-3.0.0.jar
[DEBUG] Ignoring unsupported script: Stack_Manipulation-2.0.1.jar
[DEBUG] Ignoring unsupported script: PointPicker_-2.0.0.jar
[DEBUG] Ignoring unsupported script: Jython_Interpreter-2.0.0-SNAPSHOT.jar
[DEBUG] Ignoring unsupported script: Fiji_Archipelago-2.0.0.jar
[DEBUG] Ignoring unsupported script: Kuwahara_Filter-2.0.0.jar
[DEBUG] Ignoring unsupported script: Samples_-2.0.1.jar
[DEBUG] Ignoring unsupported script: Linear_Kuwahara-2.0.0.jar
[DEBUG] Ignoring unsupported script: Macros/batch_convert_any_to_tif.txt
[DEBUG] Ignoring unsupported script: IO_-3.0.1.jar
[DEBUG] Ignoring unsupported script: M_I_P-2.0.0.jar
[DEBUG] Ignoring unsupported script: Colocalisation_Analysis-2.2.1.jar
[DEBUG] Ignoring unsupported script: Statistical_Region_Merging-2.0.0.jar
[DEBUG] Ignoring unsupported script: Time_Stamper-2.0.0.jar
[DEBUG] Ignoring unsupported script: TurboReg_-2.0.0.jar
[DEBUG] Ignoring unsupported script: Arrow_-2.0.1.jar
[DEBUG] Ignoring unsupported script: Image_Expression_Parser-3.0.0.jar
[DEBUG] Ignoring unsupported script: Macros/RGB_Histogram.txt
[DEBUG] Ignoring unsupported script: Image_5D-2.0.1.jar
[DEBUG] Ignoring unsupported script: CorrectBleach_-2.0.1.jar
[DEBUG] Ignoring unsupported script: Interactive_3D_Surface_Plot-2.4.1.jar
[DEBUG] Ignoring unsupported script: Fiji_Package_Maker-2.1.0.jar
[DEBUG] Ignoring unsupported script: 3D_Objects_Counter-2.0.0.jar
[DEBUG] Ignoring unsupported script: Clojure_Interpreter-2.0.0-SNAPSHOT.jar
[DEBUG] Ignoring unsupported script: Sync_Win-1.7-fiji3.jar
[DEBUG] Ignoring unsupported script: readme.txt
[DEBUG] Ignoring unsupported script: Calculator_Plus-2.0.0.jar
[DEBUG] Ignoring unsupported script: ToAST_-25.0.1.jar
[DEBUG] Ignoring unsupported script: z_spacing-0.0.1-SNAPSHOT.jar
[DEBUG] Ignoring unsupported script: JRuby_Interpreter-2.0.0-SNAPSHOT.jar
[DEBUG] Ignoring unsupported script: PIV_analyser-1.1.1.jar
[DEBUG] Ignoring unsupported script: level_sets-1.0.1.jar
[DEBUG] Ignoring unsupported script: Analyze/Measure_RGB.txt
[DEBUG] Ignoring unsupported script: SplineDeformationGenerator_-2.0.0.jar
[DEBUG] Ignoring unsupported script: Reconstruct_Reader-2.0.2.jar
[DEBUG] Ignoring unsupported script: MosaicJ_-2.0.0.jar
[DEBUG] Ignoring unsupported script: Sholl_Analysis-3.6.9.jar
[DEBUG] Ignoring unsupported script: IJ_Robot-2.0.0.jar
[DEBUG] Ignoring unsupported script: Multi_Kymograph-2.0.0.jar
[DEBUG] Ignoring unsupported script: Color_Inspector_3D-2.3.1.jar
[DEBUG] Ignoring unsupported script: SPIM_Registration-5.0.8.jar
[DEBUG] Ignoring unsupported script: Volume_Viewer-2.01.1.jar
[DEBUG] Ignoring unsupported script: Vaa3d_Writer-1.0.1.jar
[DEBUG] Ignoring unsupported script: 3D_Blob_Segmentation-3.0.0.jar
[DEBUG] Ignoring unsupported script: Algorithm_Launcher.jar
[DEBUG] Ignoring unsupported script: FS_Align_TrakEM2-2.0.1.jar
[DEBUG] Ignoring unsupported script: TrackMate_-3.4.2.jar
[DEBUG] Ignoring unsupported script: Directionality_-2.0.1.jar
[DEBUG] Ignoring unsupported script: mpicbg_-1.1.1.jar
[DEBUG] Ignoring unsupported script: 3D_Viewer-4.0.1.jar
[DEBUG] Ignoring unsupported script: LocalThickness_-4.0.1.jar
[DEBUG] Ignoring unsupported script: Fiji_Developer-2.0.5.jar
[DEBUG] Ignoring unsupported script: Anisotropic_Diffusion_2D-2.0.0.jar
[DEBUG] Ignoring unsupported script: Macros/About_Plugin_Macros.txt
[DEBUG] Ignoring unsupported script: Skeletonize3D_-2.1.0.jar
[DEBUG] Ignoring unsupported script: Volume_Calculator-2.0.1.jar
[DEBUG] Ignoring unsupported script: bigwarp_fiji-2.1.5.jar
[DEBUG] Ignoring unsupported script: FlowJ_-1.29.2.jar
[DEBUG] Ignoring unsupported script: Stitching_-3.1.1.jar
[DEBUG] Ignoring unsupported script: Snakuscule_-2.0.0.jar
[DEBUG] Ignoring unsupported script: StackReg_-2.0.0.jar
[DEBUG] Ignoring unsupported script: Feature_Detection-2.0.1.jar
[DEBUG] Ignoring unsupported script: Lasso_and_Blow_Tool-2.0.1.jar
[DEBUG] Ignoring unsupported script: UnwarpJ_-2.0.0.jar
[DEBUG] Ignoring unsupported script: BeanShell_Interpreter-2.0.0-SNAPSHOT.jar
[DEBUG] Ignoring unsupported script: ij-ImageIO_.jar
[DEBUG] Ignoring unsupported script: RATS_-2.0.0.jar
[DEBUG] Ignoring unsupported script: CPU_Meter-2.0.0.jar
[DEBUG] Ignoring unsupported script: MTrack2_-2.0.0.jar
[DEBUG] Ignoring unsupported script: Thread_Killer-2.0.0.jar
[DEBUG] Ignoring unsupported script: Trainable_Segmentation-3.2.2.jar
[DEBUG] Ignoring unsupported script: Video_Editing-2.0.0.jar
[DEBUG] Ignoring unsupported script: TopoJ_-2.0.0.jar
[DEBUG] Ignoring unsupported script: Utilities/Close_All_Without_Saving.txt
[DEBUG] Ignoring unsupported script: bio-formats_plugins-5.3.0.jar
[DEBUG] Ignoring unsupported script: SPIM_Opener-2.0.1.jar
[DEBUG] Found 66 scripts
[DEBUG] Created service 'net.imagej.legacy.LegacyService' in 2593 ms
[DEBUG] Created service 'net.imagej.legacy.LegacyConsoleService' in 2595 ms
[DEBUG] Creating service: fiji.DefaultFijiService
[DEBUG] Created service 'fiji.DefaultFijiService' in 1 ms
[DEBUG] Creating service: org.scijava.console.DefaultConsoleService
[DEBUG] Created service 'org.scijava.console.DefaultConsoleService' in 2 ms
[DEBUG] Creating service: org.scijava.event.DefaultEventHistory
[DEBUG] Created service 'org.scijava.event.DefaultEventHistory' in 2 ms
[DEBUG] Creating service: org.scijava.input.DefaultInputService
[DEBUG] Created service 'org.scijava.input.DefaultInputService' in 3 ms
[DEBUG] Creating service: org.scijava.io.DefaultDataHandleService
[DEBUG] Found 1 DataHandle plugins.
[DEBUG] Created service 'org.scijava.io.DefaultDataHandleService' in 1 ms
[DEBUG] Creating service: org.scijava.io.DefaultIOService
[DEBUG] Created service 'org.scijava.io.DefaultIOService' in 2 ms
[DEBUG] Creating service: org.scijava.io.DefaultRecentFileService
Mar 15, 2017 10:03:24 AM java.util.prefs.WindowsPreferences <init>
WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0
x80000002. Windows RegCreateKeyEx(...) returned error code 5.
[DEBUG] Created service 'org.scijava.io.DefaultRecentFileService' in 9 ms
[DEBUG] Creating service: org.scijava.main.DefaultMainService
[DEBUG] Created service 'org.scijava.main.DefaultMainService' in 0 ms
[DEBUG] Creating service: org.scijava.platform.DefaultPlatformService
[DEBUG] Creating service: org.scijava.platform.DefaultAppEventService
[DEBUG] Created service 'org.scijava.platform.DefaultAppEventService' in 0 ms
[DEBUG] Found 2 Platform plugins.
[DEBUG] Configuring platform: org.scijava.plugins.platforms.windows.WindowsPlatf
orm
[DEBUG] Configuring platform: org.scijava.platform.DefaultPlatform
[DEBUG] Created service 'org.scijava.platform.DefaultPlatformService' in 6 ms
[DEBUG] Creating service: org.scijava.plugins.scripting.jython.DefaultJythonServ
ice
[DEBUG] Created service 'org.scijava.plugins.scripting.jython.DefaultJythonServi
ce' in 1 ms
[DEBUG] Creating service: org.scijava.run.DefaultRunService
[DEBUG] Created service 'org.scijava.run.DefaultRunService' in 0 ms
[DEBUG] Creating service: org.scijava.script.DefaultScriptHeaderService
[DEBUG] Created service 'org.scijava.script.DefaultScriptHeaderService' in 0 ms
[DEBUG] Creating service: org.scijava.text.DefaultTextService
[DEBUG] Created service 'org.scijava.text.DefaultTextService' in 0 ms
[DEBUG] Creating service: org.scijava.tool.DefaultToolService
[DEBUG] Created service 'org.scijava.tool.DefaultToolService' in 3 ms
[DEBUG] Creating service: org.scijava.ui.DefaultUIService
[DEBUG] Created service 'org.scijava.ui.DefaultUIService' in 3 ms
[DEBUG] Creating service: org.scijava.ui.dnd.DefaultDragAndDropService
[DEBUG] Created service 'org.scijava.ui.dnd.DefaultDragAndDropService' in 2 ms
[DEBUG] Creating service: org.scijava.ui.swing.SwingIconService
[DEBUG] Created service 'org.scijava.ui.swing.SwingIconService' in 1 ms
[DEBUG] Creating service: org.scijava.ui.swing.script.DefaultLanguageSupportServ
ice
[DEBUG] Created service 'org.scijava.ui.swing.script.DefaultLanguageSupportServi
ce' in 0 ms
[DEBUG] Creating service: org.scijava.welcome.DefaultWelcomeService
[DEBUG] Created service 'org.scijava.welcome.DefaultWelcomeService' in 0 ms
[DEBUG] Creating service: org.scijava.widget.DefaultWidgetService
[DEBUG] Found 22 InputWidget plugins.
[DEBUG] Created service 'org.scijava.widget.DefaultWidgetService' in 1 ms
[DEBUG] Creating service: org.scijava.cache.DefaultCacheService
[DEBUG] Created service 'org.scijava.cache.DefaultCacheService' in 0 ms
[DEBUG] Creating service: io.scif.DefaultMetadataService
[DEBUG] Created service 'io.scif.DefaultMetadataService' in 0 ms
[DEBUG] Creating service: io.scif.codec.DefaultCodecService
[DEBUG] Created service 'io.scif.codec.DefaultCodecService' in 1 ms
[DEBUG] Creating service: io.scif.formats.qt.DefaultQTJavaService
[DEBUG] Created service 'io.scif.formats.qt.DefaultQTJavaService' in 3 ms
[DEBUG] Creating service: io.scif.formats.tiff.DefaultTiffService
[DEBUG] Created service 'io.scif.formats.tiff.DefaultTiffService' in 2 ms
[DEBUG] Creating service: io.scif.gui.DefaultGUIService
[DEBUG] Created service 'io.scif.gui.DefaultGUIService' in 1 ms
[DEBUG] Creating service: io.scif.img.DefaultImgUtilityService
[DEBUG] Created service 'io.scif.img.DefaultImgUtilityService' in 6 ms
[DEBUG] Creating service: io.scif.img.cell.cache.MapDBCache
[DEBUG] Creating service: io.scif.refs.DefaultRefManagerService
[DEBUG] Created service 'io.scif.refs.DefaultRefManagerService' in 0 ms
[DEBUG] Created service 'io.scif.img.cell.cache.MapDBCache' in 8 ms
[DEBUG] Creating service: io.scif.img.converters.DefaultPlaneConverterService
[DEBUG] Created service 'io.scif.img.converters.DefaultPlaneConverterService' in
 0 ms
[DEBUG] Creating service: io.scif.io.DefaultNIOService
[DEBUG] Created service 'io.scif.io.DefaultNIOService' in 1 ms
[DEBUG] Creating service: io.scif.ome.services.DefaultOMEMetadataService
Error while executing the main() method of class 'net.imagej.Main':
java.lang.IllegalArgumentException: Invalid service: io.scif.ome.services.Defaul
tOMEMetadataService
        at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.ja
va:280)
        at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)

        at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)

        at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166
)
        at org.scijava.Context.<init>(Context.java:278)
        at org.scijava.Context.<init>(Context.java:234)
        at org.scijava.Context.<init>(Context.java:174)
        at org.scijava.Context.<init>(Context.java:160)
        at net.imagej.ImageJ.<init>(ImageJ.java:76)
        at net.imagej.Main.launch(Main.java:61)
        at net.imagej.Main.main(Main.java:68)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.
java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
sorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:497)
        at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:279)
        at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
        at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
Caused by: java.lang.NoClassDefFoundError: ome/xml/model/enums/EnumerationExcept
ion
        at java.lang.Class.getDeclaredConstructors0(Native Method)
        at java.lang.Class.privateGetDeclaredConstructors(Class.java:2671)
        at java.lang.Class.getConstructor0(Class.java:3075)
        at java.lang.Class.newInstance(Class.java:412)
        at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHel
per.java:302)
        at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.ja
va:269)
        ... 17 more
Caused by: java.lang.ClassNotFoundException: ome.xml.model.enums.EnumerationExce
ption
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 23 more

May there be a quick solution available - like jumping back to a former version of the installer? Just to make the downloaded Fiji work again until this bug is fixed?

Cheers, Robert

ctrueden commented 7 years ago

@haesleinhuepf Sorry this slipped through the cracks.

Do you still experience this issue? Or was it transient? Please close this issue if the problem no longer happens.

FWIW, that error message indicates some version skew due to some recent(ish) Bio-Formats library renames. But I didn't know such problems hit the Java-8 update site directly. It was only a problem (to my knowledge) when the Bio-Formats update site was enabled. And that should also be fixed now.

Claus1 commented 6 years ago

The issue still exist when I try to compile latest Fiji jars with my program and new ImageJ() causes the problem. I do not need bioformat . What I have to delete? Deleting bio-formats folder does not help!

ctrueden commented 6 years ago

@Claus1 This is not the same issue. What you are talking about is something from a development environment, no? Whereas this issue was about the binary Fiji distribution not working out of the box. Please post your question on the ImageJ Forum and be specific. See Bug reporting best practices for tips on how to write a good bug report.

Claus1 commented 6 years ago

What you are talking about is something from a development environment, no?

I think no. I try to use jars from Fiji and they work wrong. ImageJ = new ImageJ() causes the same issue with

java.lang.IllegalArgumentException: Invalid service: io.scif.ome.services.Defaul tOMEMetadataService at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.ja va:280)

Pure ImageJ 2 rc46 binary installation from the site works ok. Only. Newest binary versions ImageJ from maven reps do not process correctly (2.0.0-rc-65) because it has some jars references from unknown libraries. That references obviously exist in maven repos but with slightly different names. It seems like nobody supports it and checks.

ctrueden commented 6 years ago

@Claus1 Happy to help if you post your question on the ImageJ Forum. Again, please describe exactly what you are trying to do. From your writeup above, I do not understand exactly what you are trying to do, or how you are attempting to do it. I do actively support the core ImageJ libraries and the newest ones should definitely be working, provided you are deploying the JARs as intended.

Claus1 commented 6 years ago

Again, please describe exactly what you are trying to do.

I try to use ImageJ from my program for filtering images without GUI. Using jar files from latest Fiji is not possible for that because the initialization issue above. May be it is wrong way to use ImageJ but binary reference in my project

net.imagej imagej 2.0.0-rc-65

is not resolved if I use instructions from the site. Some referenced libraries are uknown for "Maven repo" at "http://repo1.maven.org/maven2", "Spring repo" at "http://repo.springsource.org/libs-release", "Apache repo" at "https://repository.apache.org/content/repositories/releases", "JBoss repo" at "http://repository.jboss.org/nexus/content/groups/public-jboss", "Sonatype repo" at "https://oss.sonatype.org/content/repositories/releases", "Mvnrepository" at "http://mvnrepository.com/artifact"

Make clean project with this dependency and will see.

ctrueden commented 6 years ago

@Claus1 Sorry that replying to this fell through the cracks for me.

From your list above, what is missing is the ImageJ Maven repository! https://maven.imagej.net/

A lot of the core ImageJ libraries, including net.imagej:imagej, are located in this repository. You need that repository in your pom.xml or similar build file for whatever build system you are using.

If you still need assistance, please push an MCVE somewhere public so that we can see exactly how your project is set up, and determine in detail what is going wrong.

is not resolved if I use instructions from the site.

Which instructions? Link, please.

Claus1 commented 6 years ago

@ctrueden I avoided the issue by making jars from Fuji sources.