I want to convert a 5D image (XYCZT format) of size 114x113x1x25x7200. I created a h5 file that I want to convert to n5 to visualize with the N5-Viewer of BigDataViewer in Fiji.
Here is the command,
n5-copy -i N00046_4D.h5 -o N00046_4D.n5
The output is the following
attributes:
/data
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Length is too large (2318760000)
at net.imglib2.cache.util.CacheAsUncheckedCacheAdapter.get(CacheAsUncheckedCacheAdapter.java:78)
at net.imglib2.img.cell.LazyCellImg$LazyCells.get(LazyCellImg.java:104)
at net.imglib2.img.list.AbstractLongListImg$LongListRandomAccess.get(AbstractLongListImg.java:274)
at net.imglib2.img.cell.CellRandomAccess.getCell(CellRandomAccess.java:142)
at net.imglib2.img.cell.CellRandomAccess.updatePosition(CellRandomAccess.java:480)
at net.imglib2.img.cell.CellRandomAccess.<init>(CellRandomAccess.java:136)
at net.imglib2.img.cell.AbstractCellImg.randomAccess(AbstractCellImg.java:104)
at net.imglib2.img.cell.AbstractCellImg.randomAccess(AbstractCellImg.java:51)
at net.imglib2.util.Util.getTypeFromInterval(Util.java:806)
at org.janelia.saalfeldlab.n5.imglib2.N5Utils.save(N5Utils.java:1367)
at org.janelia.saalfeldlab.Copy.copyDataset(Copy.java:262)
at org.janelia.saalfeldlab.Copy.copyGroup(Copy.java:311)
at org.janelia.saalfeldlab.Copy.call(Copy.java:356)
at org.janelia.saalfeldlab.Copy.call(Copy.java:157)
at picocli.CommandLine.executeUserObject(CommandLine.java:1853)
at picocli.CommandLine.access$1100(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2255)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2249)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2213)
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2080)
at picocli.CommandLine.execute(CommandLine.java:1978)
at org.janelia.saalfeldlab.Copy.main(Copy.java:200)
Caused by: java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Length is too large (2318760000)
at net.imglib2.cache.ref.SoftRefLoaderCache.get(SoftRefLoaderCache.java:145)
at net.imglib2.cache.util.LoaderCacheAsCacheAdapter.get(LoaderCacheAsCacheAdapter.java:76)
at net.imglib2.cache.util.CacheAsUncheckedCacheAdapter.get(CacheAsUncheckedCacheAdapter.java:74)
... 21 more
Caused by: java.lang.IllegalArgumentException: Length is too large (2318760000)
at ch.systemsx.cisd.base.mdarray.MDAbstractArray.getLength(MDAbstractArray.java:422)
at ch.systemsx.cisd.base.mdarray.MDAbstractArray.getLength(MDAbstractArray.java:396)
at ch.systemsx.cisd.hdf5.HDF5BaseReader.tryGetSpaceParameters(HDF5BaseReader.java:724)
at ch.systemsx.cisd.hdf5.HDF5BaseReader.getSpaceParameters(HDF5BaseReader.java:671)
at ch.systemsx.cisd.hdf5.HDF5UnsignedShortReader$15.call(HDF5UnsignedShortReader.java:871)
at ch.systemsx.cisd.hdf5.HDF5UnsignedShortReader$15.call(HDF5UnsignedShortReader.java:1)
at ch.systemsx.cisd.hdf5.cleanup.CleanUpCallable.call(CleanUpCallable.java:40)
at ch.systemsx.cisd.hdf5.HDF5UnsignedShortReader.readMDArrayBlockWithOffset(HDF5UnsignedShortReader.java:895)
at org.janelia.saalfeldlab.n5.hdf5.N5HDF5Reader.readBlock(N5HDF5Reader.java:736)
at org.janelia.saalfeldlab.n5.imglib2.N5CacheLoader.get(N5CacheLoader.java:117)
at org.janelia.saalfeldlab.n5.imglib2.N5CacheLoader.get(N5CacheLoader.java:87)
at net.imglib2.cache.ref.SoftRefLoaderCache.get(SoftRefLoaderCache.java:135)
... 23 more
I want to convert a 5D image (XYCZT format) of size 114x113x1x25x7200. I created a h5 file that I want to convert to n5 to visualize with the N5-Viewer of BigDataViewer in Fiji. Here is the command,
The output is the following
The file is located here,