Java Exception when opening a large (1.5 Gb) tiff

[Taylor_B]

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.

[Mark Hiner]

Hello,

 This is likely a bug that can be resolved by turning off all the options
in "Edit > Options > ImageJ2". If that doesn't fix things for you, please
let us know.

 Also, if you would be willing to share your dataset so we can figure out
what went wrong, you can upload it via "Help > Upload Sample Image" in Fiji.

Regards,
Mark

On Mon, Sep 1, 2014 at 2:07 PM, Taylor_B <[hidden email]> wrote:

> 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.
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Java-Exception-when-opening-a-large-1-5-Gb-tiff-tp5009451.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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