Opening a File with ImageJ - Exception message

[Carlos Alberto Perez]

Hello everyone,

An exception message appears when I try to open a particular tif file with
ImageJ. It is an image of 16Mb in size. O popup window appears with the
following message:

 

“java.lang.ArrayIndexOutOfBoundsException”

 

Does anyone may explain me what kind of problem is this and if I can fix it.

Thank you in advance

Carlos.

 

Carlos A. Pérez, PhD

X-Ray Fluorescence and Absorption Group

LNLS -Brazilian Synchrotron Light Source Laboratory

http://www.lnls.br

Phone: [phone]

Fax: [phone]

Mail address:
Caixa Postal 6192
CEP 13083-970
Campinas - SP, Brazil



 

[dscho]

Hi Carlos,

On Wed, 4 Apr 2012, Carlos Alberto Perez wrote:

> An exception message appears when I try to open a particular tif file
> with ImageJ. It is an image of 16Mb in size. O popup window appears with
> the following message:
>
> ?java.lang.ArrayIndexOutOfBoundsException?

Have you tried Bio-Formats? You can download it from
http://loci.wisc.edu/software/bio-formats

Ciao,
Johannes

[ctrueden]

Hi Carlos,

An exception message appears when I try to open a particular tif file with
>
 ImageJ. It is an image of 16Mb in size.
>

Depending on the file format, a different plugin will be used to open. So
it is not clear which plugin is emitting the error message you are seeing.

Did you try opening with the Bio-Formats Importer plugin?

If you install the Fiji distribution of ImageJ (http://fiji.sc/)
Bio-Formats is bundled with it. Otherwise, you can download it yourself:
http://loci.wisc.edu/bio-formats/imagej

Using Bio-Formats, you should at least get a more informative error message
if there is a problem. Feel free to reply back to the list with more
details if you continue to have trouble.

Regards,
Curtis


On Wed, Apr 4, 2012 at 12:06 PM, Carlos Alberto Perez <[hidden email]> wrote:

> Hello everyone,
>
> An exception message appears when I try to open a particular tif file with
> ImageJ. It is an image of 16Mb in size. O popup window appears with the
> following message:
>
>
>
> “java.lang.ArrayIndexOutOfBoundsException”
>
>
>
> Does anyone may explain me what kind of problem is this and if I can fix
> it.
>
> Thank you in advance
>
> Carlos.
>
>
>
> Carlos A. Pérez, PhD
>
> X-Ray Fluorescence and Absorption Group
>
> LNLS -Brazilian Synchrotron Light Source Laboratory
>
> http://www.lnls.br
>
> Phone: [phone]
>
> Fax: [phone]
>
> Mail address:
> Caixa Postal 6192
> CEP 13083-970
> Campinas - SP, Brazil
>
>
>
>
>

[Carlos Alberto Perez]

Hi all,
Thank you to all for a quick answer giving me support to this problem. I
installed the LOCI plugins as was suggested by many of you and it was
possible to open the file using bio-formats.
Regards,
Carlos


Carlos A. Pérez, PhD
X-Ray Fluorescence and Absorption Group
LNLS -Brazilian Synchrotron Light Source Laboratory
http://www.lnls.br
Phone: [phone]
Fax: [phone]
Mail address:
Caixa Postal 6192
CEP 13083-970
Campinas - SP, Brazil



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis
Rueden
Sent: quarta-feira, 4 de abril de 2012 14:56
To: [hidden email]
Subject: Re: Opening a File with ImageJ - Exception message

Hi Carlos,

An exception message appears when I try to open a particular tif file with
>
 ImageJ. It is an image of 16Mb in size.
>

Depending on the file format, a different plugin will be used to open. So it
is not clear which plugin is emitting the error message you are seeing.

Did you try opening with the Bio-Formats Importer plugin?

If you install the Fiji distribution of ImageJ (http://fiji.sc/) Bio-Formats
is bundled with it. Otherwise, you can download it yourself:
http://loci.wisc.edu/bio-formats/imagej

Using Bio-Formats, you should at least get a more informative error message
if there is a problem. Feel free to reply back to the list with more details
if you continue to have trouble.

Regards,
Curtis


On Wed, Apr 4, 2012 at 12:06 PM, Carlos Alberto Perez <[hidden email]> wrote:

> Hello everyone,
>
> An exception message appears when I try to open a particular tif file
> with ImageJ. It is an image of 16Mb in size. O popup window appears
> with the following message:
>
>
>
> “java.lang.ArrayIndexOutOfBoundsException”
>
>
>
> Does anyone may explain me what kind of problem is this and if I can
> fix it.
>
> Thank you in advance
>
> Carlos.
>
>
>
> Carlos A. Pérez, PhD
>
> X-Ray Fluorescence and Absorption Group
>
> LNLS -Brazilian Synchrotron Light Source Laboratory
>
> http://www.lnls.br
>
> Phone: [phone]
>
> Fax: [phone]
>
> Mail address:
> Caixa Postal 6192
> CEP 13083-970
> Campinas - SP, Brazil
>
>
>
>
>

[ima258]

Hi all... i am newbie here..I have a quite similar problem with carlos, there have an exception when i run the plugin. I downloaded bioformat, but i think it help less for my work. actually i try to run my lecturer's plugin for certain dedicated function. my working files are in jpg and dcm format with less than 1000kb. Here are the problem when i open the plugin:

 ImageJ 1.49t; Java 1.8.0_45 [64-bit]; Windows 8 6.2; 14MB of 2988MB (<1%)
 
java.lang.StringIndexOutOfBoundsException: String index out of range: -1
        at java.lang.String.substring(String.java:1955)
        at ImageCanvasPaintImplant.scaleImplantAndDICOM(JImplant_Loader2.java:522)
        at ImageCanvasPaintImplant.<init>(JImplant_Loader2.java:60)
        at JImplant_Loader2.run(JImplant_Loader2.java:47)
        at ij.IJ.runUserPlugIn(IJ.java:199)
        at ij.IJ.runUserPlugIn(IJ.java:212)
        at ij.IJ.runPlugIn(IJ.java:163)
        at ij.Executer.runCommand(Executer.java:131)
        at ij.Executer.run(Executer.java:64)
        at java.lang.Thread.run(Thread.java:745)

Can anyone assist me with this problem?