Fiji: Importing of ASCII data fails

[hvdosten]

Hi out there,

up to now I had no problem importing ASCII data into Fiji. But since the
last update it seems no more to be possible to import data files...

This is an example of those data:

P2
  480   400
255
#
255
255
255
255
:
:
149
148
135
140
166
140


What can I do now? The data are fine, which means that there are no crazy
characters in the file or so...



This is the error message:


Fiji/ImageJ 1.47n; Java 1.6.0_43 [64-bit]; Mac OS X 10.8.3; 20MB of 4409MB
(<1%)

java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at ij.Command.runPlugIn(Command.java:148)
at ij.Command.runCommand(Command.java:97)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.ArrayIndexOutOfBoundsException





Thanks a lot for any hint!!

Harald

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[Adrian Daerr-2]

> up to now I had no problem importing ASCII data into Fiji.

 From what follows it seems you are talking more specifically about
portable grey map (PGM) images (rather than any ASCII text file).

> java.lang.reflect.InvocationTargetException
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at ij.Command.runPlugIn(Command.java:148)
> at ij.Command.runCommand(Command.java:97)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:680)
> Caused by: java.lang.ArrayIndexOutOfBoundsException

Can you also show the debug output (check Edit->Options->Misc...->Debug
mode, try to open your image, and check the Log window), to see which
plug-in is run (it should be ij.plugin.PGM_Reader) ?

I just tried with an up-to-date Fiji on Linux and had no issues with a
PGM (P2) file like yours. As Fiji can open these out of the box, you
could download a fresh Fiji to quickly check whether the bug resides
with Fiji-on-MacOSX in general or with your own installation.

good luck
Adrian

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[dscho]

Hi,

On Wed, 10 Apr 2013, Dr. Harald von der Osten wrote:

> up to now I had no problem importing ASCII data into Fiji. But since the
> last update it seems no more to be possible to import data files...
>
> This is an example of those data:
>
> P2
>   480   400
> 255
> 255
> 255
> 255
> 255
> :
> :
> 149
> 148
> 135
> 140
> 166
> 140
>
>
> What can I do now? The data are fine, which means that there are no crazy
> characters in the file or so...
>
>
>
> This is the error message:
>
>
> Fiji/ImageJ 1.47n; Java 1.6.0_43 [64-bit]; Mac OS X 10.8.3; 20MB of 4409MB
> (<1%)
>
> java.lang.reflect.InvocationTargetException
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at ij.Command.runPlugIn(Command.java:148)
> at ij.Command.runCommand(Command.java:97)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:680)
> Caused by: java.lang.ArrayIndexOutOfBoundsException

You could try downgrading via Help-Update ImageJ. Hopefully you will be
able to find a version that works!

Ciao,
Johannes

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