Problem in opening a file

[aparna sadananda]

Hi all,
I have a movie in oib format with a size of 24.5 MB. I have allotted a
memory of 1500 MB to Image J. But still, this file does not open. instead a
window opens up with the following:

 java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 999
 at java.util.Vector.get(Unknown Source)
 at loci.formats.in.FV1000Reader.openBytes(FV1000Reader.java:163)
 at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:140)
 at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:113)
 at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:187)
 at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:214)
 at loci.plugins.Util.openProcessors(Util.java:104)
 at loci.plugins.Importer.run(Importer.java:525)
 at loci.plugins.LociImporter.run(LociImporter.java:72)
 at ij.IJ.runUserPlugIn(IJ.java:177)
 at ij.IJ.runPlugIn(IJ.java:143)
 at ij.IJ.runPlugIn(IJ.java:131)
 at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:253)
 at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
 at ij.IJ.runUserPlugIn(IJ.java:177)
 at ij.IJ.runPlugIn(IJ.java:143)
 at ij.IJ.runPlugIn(IJ.java:131)
 at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:337)
 at ij.io.Opener.openImage(Opener.java:245)
 at ij.io.Opener.openImage(Opener.java:268)
 at ij.io.Opener.open(Opener.java:124)
 at ij.io.Opener.open(Opener.java:63)
 at ij.plugin.Commands.run(Commands.java:23)
 at ij.IJ.runPlugIn(IJ.java:150)
 at ij.Executer.runCommand(Executer.java:120)
 at ij.Executer.run(Executer.java:58)
 at java.lang.Thread.run(Unknown Source)
It is weird because another oib file of size 23.5 MB opens without any
problem. This is a movie of 240 frames in 512* 512 pixel format. And the one
that does not open is of 1200 frames but 100*24 pixel format.

What could be going wrong? Many thanks in advance to anyone who helps me
with this!
Aparna

[ctrueden]

Hi Aparna,

It's not a memory issue; it's a bug in Bio-Formats. If you would be willing
to send us the file, we can look into fixing the problem. You can use our
FTP server (info sent in another email offline).

-Curtis

On Tue, Nov 10, 2009 at 10:51 AM, aparna sadananda <
[hidden email]> wrote:

> Hi all,
> I have a movie in oib format with a size of 24.5 MB. I have allotted a
> memory of 1500 MB to Image J. But still, this file does not open. instead a
> window opens up with the following:
>
>  java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 999
>  at java.util.Vector.get(Unknown Source)
>  at loci.formats.in.FV1000Reader.openBytes(FV1000Reader.java:163)
>  at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:140)
>  at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:113)
>  at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:187)
>  at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:214)
>  at loci.plugins.Util.openProcessors(Util.java:104)
>  at loci.plugins.Importer.run(Importer.java:525)
>  at loci.plugins.LociImporter.run(LociImporter.java:72)
>  at ij.IJ.runUserPlugIn(IJ.java:177)
>  at ij.IJ.runPlugIn(IJ.java:143)
>  at ij.IJ.runPlugIn(IJ.java:131)
>  at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:253)
>  at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
>  at ij.IJ.runUserPlugIn(IJ.java:177)
>  at ij.IJ.runPlugIn(IJ.java:143)
>  at ij.IJ.runPlugIn(IJ.java:131)
>  at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:337)
>  at ij.io.Opener.openImage(Opener.java:245)
>  at ij.io.Opener.openImage(Opener.java:268)
>  at ij.io.Opener.open(Opener.java:124)
>  at ij.io.Opener.open(Opener.java:63)
>  at ij.plugin.Commands.run(Commands.java:23)
>  at ij.IJ.runPlugIn(IJ.java:150)
>  at ij.Executer.runCommand(Executer.java:120)
>  at ij.Executer.run(Executer.java:58)
>  at java.lang.Thread.run(Unknown Source)
> It is weird because another oib file of size 23.5 MB opens without any
> problem. This is a movie of 240 frames in 512* 512 pixel format. And the
> one
> that does not open is of 1200 frames but 100*24 pixel format.
>
> What could be going wrong? Many thanks in advance to anyone who helps me
> with this!
> Aparna
>

[Melissa Linkert-2]

Hi Aparna,

From the error message, it looks like you are using an old version of
Bio-Formats.  Before you send a file, I would recommend that you
update to the latest stable release (4.1) and try to open the file
again.  You can download the latest release from
http://loci.wisc.edu/ome/formats-download.html.

Regards,
-Melissa

On Tue, Nov 10, 2009 at 10:51 AM, aparna sadananda
<[hidden email]> wrote:

> Hi all,
> I have a movie in oib format with a size of 24.5 MB. I have allotted a
> memory of 1500 MB to Image J. But still, this file does not open. instead a
> window opens up with the following:
>
>  java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 999
>  at java.util.Vector.get(Unknown Source)
>  at loci.formats.in.FV1000Reader.openBytes(FV1000Reader.java:163)
>  at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:140)
>  at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:113)
>  at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:187)
>  at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:214)
>  at loci.plugins.Util.openProcessors(Util.java:104)
>  at loci.plugins.Importer.run(Importer.java:525)
>  at loci.plugins.LociImporter.run(LociImporter.java:72)
>  at ij.IJ.runUserPlugIn(IJ.java:177)
>  at ij.IJ.runPlugIn(IJ.java:143)
>  at ij.IJ.runPlugIn(IJ.java:131)
>  at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:253)
>  at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
>  at ij.IJ.runUserPlugIn(IJ.java:177)
>  at ij.IJ.runPlugIn(IJ.java:143)
>  at ij.IJ.runPlugIn(IJ.java:131)
>  at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:337)
>  at ij.io.Opener.openImage(Opener.java:245)
>  at ij.io.Opener.openImage(Opener.java:268)
>  at ij.io.Opener.open(Opener.java:124)
>  at ij.io.Opener.open(Opener.java:63)
>  at ij.plugin.Commands.run(Commands.java:23)
>  at ij.IJ.runPlugIn(IJ.java:150)
>  at ij.Executer.runCommand(Executer.java:120)
>  at ij.Executer.run(Executer.java:58)
>  at java.lang.Thread.run(Unknown Source)
> It is weird because another oib file of size 23.5 MB opens without any
> problem. This is a movie of 240 frames in 512* 512 pixel format. And the one
> that does not open is of 1200 frames but 100*24 pixel format.
>
> What could be going wrong? Many thanks in advance to anyone who helps me
> with this!
> Aparna
>