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Tests in the datasetCheck package crash

Tests in the datasetCheck package crash when run with other tests classes, but pass when run by themselves. This is somehow related to the incompatibility issues between ImageJ1 and ImageJ2. All test cases crash with:

java.lang.ExceptionInInitializerError
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at org.junit.runners.BlockJUnit4ClassRunner.createTest(BlockJUnit4ClassRunner.java:217)
    at org.junit.runners.BlockJUnit4ClassRunner$1.runReflectiveCall(BlockJUnit4ClassRunner.java:266)
    at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
    at org.junit.runners.BlockJUnit4ClassRunner.methodBlock(BlockJUnit4ClassRunner.java:263)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
    at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
    at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
    at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
    at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
    at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
    at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
    at org.junit.runners.Suite.runChild(Suite.java:128)
    at org.junit.runners.Suite.runChild(Suite.java:27)
    at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
    at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
    at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
    at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
    at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
    at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
    at org.junit.runner.JUnitCore.run(JUnitCore.java:137)
    at com.intellij.junit4.JUnit4IdeaTestRunner.startRunnerWithArgs(JUnit4IdeaTestRunner.java:117)
    at com.intellij.rt.execution.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:234)
    at com.intellij.rt.execution.junit.JUnitStarter.main(JUnitStarter.java:74)
    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:498)
    at com.intellij.rt.execution.application.AppMain.main(AppMain.java:144)
Caused by: java.lang.IllegalArgumentException: Invalid service: net.imagej.legacy.LegacyConsoleService
    at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java: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:277)
    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:79)
    at protoOps.datasetCheck.TestDatasetIs3D.<clinit>(TestDatasetIs3D.java:20)
    ... 33 more
Caused by: java.lang.IllegalArgumentException: Invalid service: net.imagej.legacy.LegacyService
    at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
    at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:340)
    at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
    ... 42 more
Caused by: java.lang.ExceptionInInitializerError
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
    at java.lang.Class.newInstance(Class.java:442)
    at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:302)
    at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
    ... 45 more
Caused by: java.lang.RuntimeException: No _hooks field found in ij.IJ
It appears that this class was already defined in the class loader!
Please make sure that you initialize the LegacyService before using
any ImageJ 1.x class. You can do that by adding this static initializer:

    static {
        LegacyInjector.preinit();
    }

To debug this issue, start the JVM with the option:

    -javaagent:/home/rdom/.m2/repository/net/imagej/ij1-patcher/0.12.3/ij1-patcher-0.12.3.jar

To enforce pre-initialization, start the JVM with the option:

    -javaagent:/home/rdom/.m2/repository/net/imagej/ij1-patcher/0.12.3/ij1-patcher-0.12.3.jar=init

    at net.imagej.patcher.CodeHacker.javaAgentHint(CodeHacker.java:828)
    at net.imagej.patcher.LegacyInjector.alreadyPatched(LegacyInjector.java:433)
    at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:380)
    at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
    at net.imagej.legacy.LegacyService.<clinit>(LegacyService.java:133)
    ... 52 more
Caused by: java.lang.NoSuchFieldException: _hooks
    at java.lang.Class.getField(Class.java:1703)
    at net.imagej.patcher.LegacyInjector.alreadyPatched(LegacyInjector.java:424)
    ... 55 more

Test image creators fail when run from Java API

All of the test image creator ops (crossed circle, cuboid, wire frame cuboid) when instantiated and run from Java. They need to inherit AbstractContextual.setContext to work properly. Also document to the class files how they can be run from Java and an opService.

VolumeFractionSurface returns wrong results with a ROIManager

VolumeFractionSurface returns the following results when run with a ROIManager:

Bone volume: 0.000 Total volume: 0.000 Ratio: NaN

The ROIManager contains one rectangular roi (0, 0, w, h) on slice number 1.

At a similar setup BoneJ1 produces the results:

Bone volume: 0.002 Total volume: 0.017 Ratio: 0.109

Test image used: binary_trabeculae_small.tif
Resampling: 6

Improve the accuracy of VolumeFractionSurface

The accuracy of the surface volume measurement could be possibly improved by ignoring mesh faces which intersect the stack edges. The reason for this is that samples are often cut from larger objects. This cutting creates cross-sectional faces, which in reality are not part of the surface area of the whole object.

VolumeFractionSurface reports wrong fraction

The surface algorithm reports that the volume fraction for every image is 1.0, e.g. bone volume equals total volume. This may have something to do with the fact that the implementation of MCTriangulator and/or CustomTriangleMesh has changed. The drawing of the surface masks seems to work.

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