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Can't open large volume #46
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Hi @kthorn and thanks for the report! The fix should be out by the end of next week. If you'd like to try a preliminary version, please let me know. |
Hi! I'm having this same problem with a 239x2560x2160 stack that's over 2 GB in size. @skalarproduktraum, you said in March 24 that a fix for this issue was going out around that time, so I'm wondering if that actually happened or if it might have been delayed? Thanks a lot for the support! |
Hi Bruno, Unfortunately the problem goes very deep and has multiple aspects: ClearVolume 2 is taking time to developp, it will be built on top of Scenery (@skalarproduktraum https://github.com/skalarproduktraum) In the meantime, Think about it, your screen has probably about 1000x2000 pixels, so A volume of 1000 x 1000 x 1000 is already a beautiful stack that will render We should probably add this automatic downscaling… Hope this helps… Cheers :-) loic
Dr. Loïc Alain Royer Post-Doc - Myers Lab Too short? Here's why: http://emailcharter.org/ |
When I try to open a 2560 x 2160 x 197 volume in ClearVolume I get the following error:
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Number of elements in Container too big, use for example CellContainer instead: 2178662400 > 2147483647
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:277)
at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Number of elements in Container too big, use for example CellContainer instead: 2178662400 > 2147483647
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:273)
... 5 more
Caused by: java.lang.RuntimeException: Number of elements in Container too big, use for example CellContainer instead: 2178662400 > 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:380)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopies(ImgLib2ClearVolume.java:354)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:446)
at de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run(ClearVolumeManager.java:182)
at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager(GenericClearVolumeGui.java:303)
at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.(GenericClearVolumeGui.java:160)
at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:86)
at org.scijava.command.CommandModule.run(CommandModule.java:205)
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)
If I crop the image to a smaller size in X and Y it opens fine.
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