Java Exception when opening a large (1.5 Gb) tiff

Posted by Taylor_B on Sep 01, 2014; 7:07pm
URL: http://imagej.273.s1.nabble.com/Java-Exception-when-opening-a-large-1-5-Gb-tiff-tp5009451.html

Hi,

When trying to open a large 16-bit RGB TIFF, I received the following exception:

"(Fiji Is Just) ImageJ 2.0.0-rc-14/1.49g; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.4; 2402MB of 6889MB (34%)
 
java.lang.ArrayIndexOutOfBoundsException: 2
        at io.scif.util.FormatTools.checkTileSize(FormatTools.java:649)
        at io.scif.util.FormatTools.checkPlaneForWriting(FormatTools.java:626)
        at io.scif.util.FormatTools.checkPlaneForReading(FormatTools.java:611)
        at io.scif.formats.MinimalTIFFFormat$Reader.openPlane(MinimalTIFFFormat.java:607)
        at io.scif.formats.MinimalTIFFFormat$Reader.openPlane(MinimalTIFFFormat.java:534)
        at io.scif.AbstractReader.openPlane(AbstractReader.java:167)
        at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:170)
        at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:151)
        at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:297)
        at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:208)
        at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:225)
        at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:191)
        at io.scif.img.ImgOpener.read(ImgOpener.java:808)
        at io.scif.img.ImgOpener.read(ImgOpener.java:793)
        at io.scif.img.ImgOpener.read(ImgOpener.java:775)
        at io.scif.img.ImgOpener.readPlanes(ImgOpener.java:761)
        at io.scif.img.ImgOpener.openImgs(ImgOpener.java:362)
        at io.scif.img.ImgOpener.openImgs(ImgOpener.java:257)
        at io.scif.img.ImgOpener.openImgs(ImgOpener.java:145)
        at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
        at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
        at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
        at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
        at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:136)
        at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:327)
        at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:150)
        at ij.IJ.runPlugIn(IJ.java)
        at ij.Executer.runCommand(Executer.java:131)
        at ij.Executer.run(Executer.java:64)
        at java.lang.Thread.run(Thread.java:695)"

I've updated ImageJ using Fiji.  Based on the header, this doesn't appear to be a memory allocation problem, but I could be wrong.  Any suggestions would be appreciated.