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Images > 2GiB are not supported #2

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skalarproduktraum opened this issue Aug 18, 2015 · 1 comment
Open

Images > 2GiB are not supported #2

skalarproduktraum opened this issue Aug 18, 2015 · 1 comment
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@fjug
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enhancement help wanted

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@skalarproduktraum
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Even if the present graphics card has enough memory, the plugin bails out with

java.lang.RuntimeException: Number of elements in Container too big, use for example CellContainer instead: 5086604250 > 2147483647
at net.imglib2.img.array.ArrayImgFactory.numEntitiesRangeCheck(ArrayImgFactory.java:71)
at net.imglib2.img.array.ArrayImgFactory.createByteInstance(ArrayImgFactory.java:79)
at net.imglib2.img.array.ArrayImgFactory.createByteInstance(ArrayImgFactory.java:58)
at de.mpicbg.jug.clearvolume.ClearVolumeUnsignedShortType.createSuitableNativeImg(ClearVolumeUnsignedShortType.java:320)
at net.imglib2.img.array.ArrayImgFactory.create(ArrayImgFactory.java:63)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopy(ImgLib2ClearVolume.java:355)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopies(ImgLib2ClearVolume.java:328)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:419)
at de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run(ClearVolumeManager.java:156)
at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager(GenericClearVolumeGui.java:208)
at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.<init>(GenericClearVolumeGui.java:135)
at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:80)
at org.scijava.command.CommandModule.run(CommandModule.java:201)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[ERROR] Module threw exception
java.lang.RuntimeException: Number of elements in Container too big, use for example CellContainer instead: 5086604250 > 2147483647
at net.imglib2.img.array.ArrayImgFactory.numEntitiesRangeCheck(ArrayImgFactory.java:71)
at net.imglib2.img.array.ArrayImgFactory.createByteInstance(ArrayImgFactory.java:79)
at net.imglib2.img.array.ArrayImgFactory.createByteInstance(ArrayImgFactory.java:58)
at de.mpicbg.jug.clearvolume.ClearVolumeUnsignedShortType.createSuitableNativeImg(ClearVolumeUnsignedShortType.java:320)
at net.imglib2.img.array.ArrayImgFactory.create(ArrayImgFactory.java:63)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopy(ImgLib2ClearVolume.java:355)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopies(ImgLib2ClearVolume.java:328)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:419)
at de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run(ClearVolumeManager.java:156)
at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager(GenericClearVolumeGui.java:208)
at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.<init>(GenericClearVolumeGui.java:135)
at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:80)
at org.scijava.command.CommandModule.run(CommandModule.java:201)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

@fjug suggested to use cell images. Maybe @tpietzsch also has some suggestions? :)

The bug was originally reported by @yafshar.
@royerloic
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Yes, that’s a limitation of the ClearVolume - imaglib2 bridge.
We need to improve that, the only way to send >2G images to
ClearVolume is via the CoreMem API. We will look into it.

On 18 Aug 2015, at 12:18, Ulrik Guenther notifications@github.com wrote:

Even if the present graphics card has enough memory, the plugin bails out with

java.lang.RuntimeException: Number of elements in Container too big, use for example CellContainer instead: 5086604250 > 2147483647
at net.imglib2.img.array.ArrayImgFactory.numEntitiesRangeCheck(ArrayImgFactory.java:71)
at net.imglib2.img.array.ArrayImgFactory.createByteInstance(ArrayImgFactory.java:79)
at net.imglib2.img.array.ArrayImgFactory.createByteInstance(ArrayImgFactory.java:58)
at de.mpicbg.jug.clearvolume.ClearVolumeUnsignedShortType.createSuitableNativeImg(ClearVolumeUnsignedShortType.java:320)
at net.imglib2.img.array.ArrayImgFactory.create(ArrayImgFactory.java:63)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopy(ImgLib2ClearVolume.java:355)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopies(ImgLib2ClearVolume.java:328)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:419)
at de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run(ClearVolumeManager.java:156)
at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager(GenericClearVolumeGui.java:208)
at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.(GenericClearVolumeGui.java:135)
at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:80)
at org.scijava.command.CommandModule.run(CommandModule.java:201)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
[ERROR] Module threw exception
java.lang.RuntimeException: Number of elements in Container too big, use for example CellContainer instead: 5086604250 > 2147483647
at net.imglib2.img.array.ArrayImgFactory.numEntitiesRangeCheck(ArrayImgFactory.java:71)
at net.imglib2.img.array.ArrayImgFactory.createByteInstance(ArrayImgFactory.java:79)
at net.imglib2.img.array.ArrayImgFactory.createByteInstance(ArrayImgFactory.java:58)
at de.mpicbg.jug.clearvolume.ClearVolumeUnsignedShortType.createSuitableNativeImg(ClearVolumeUnsignedShortType.java:320)
at net.imglib2.img.array.ArrayImgFactory.create(ArrayImgFactory.java:63)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopy(ImgLib2ClearVolume.java:355)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopies(ImgLib2ClearVolume.java:328)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:419)
at de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run(ClearVolumeManager.java:156)
at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager(GenericClearVolumeGui.java:208)
at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.(GenericClearVolumeGui.java:135)
at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:80)
at org.scijava.command.CommandModule.run(CommandModule.java:201)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
@fjug https://github.com/fjug suggested to use cell images. Maybe @tpietzsch https://github.com/tpietzsch also has some suggestions? :)

The bug was originally reported by @yafshar https://github.com/yafshar.

—
Reply to this email directly or view it on GitHub #2.

Dr. Loïc Alain Royer

Post-Doc - Myers Lab
Max Planck Institute
of Molecular Cell Biology
and Genetics
Pfotenhauerstr. 108
01307 Dresden

Too short? Here's why: http://emailcharter.org/

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@skalarproduktraum @royerloic @fjug