| IDL Java Bridge and bio-format [message #86079] |
Mon, 30 September 2013 14:17  |
biophys
Messages: 68
Registered: July 2004
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Hi, Folks
I have been trying to use bio-format via java bridge with IDL 8.2.3 under 64bit windows 7. And I am getting "Exception thrown java.lang.NullPointerException" during objnew() call to create the loci.format.ImageReader class. I also tried to enable logging and only get the following
##############jb_log15000.txt#################
IDL-Java Bridge : May 3 2013 01:45:38
Log Location : C:/Users/bp/idl_source/lab/bioformat/java/LOG/
Bridge Logging : CONFIGFINE
Config file : C:\Users\bp\idl_source\lab\bioformat\java\idljavabrc
Exit Strategy : <null>
Restart Bridge : FALSE
EXCEPTION cJBExceptJavaException : NewObjectA
ERR <IDL_JBCreateJavaObject return=0000000000000000
The bio-format distribution of both 4.4.8 and 4.4.9 worked perfectly in ImageJ(Fiji). So I guess the problem is most likely the java bridge. But I don't know how to pursue further at this point. Any suggestions is highly appreciated!
Thank you,
BP
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| Re: IDL Java Bridge and bio-format [message #86082 is a reply to message #86079] |
Mon, 30 September 2013 17:03  |
biophys
Messages: 68
Registered: July 2004
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Member |
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A bit more details for you guys to reproduce the error.
1. visit Bio-format website
http://www.openmicroscopy.org/site/products/bio-formats
2. download the loci_tools.jar file and save to path\to\myjava\.
http://cvs.openmicroscopy.org.uk/snapshots/bioformats/4.4.8/ loci_tools.jar
or
http://hudson.openmicroscopy.org.uk/job/BIOFORMATS-daily/las tSuccessfulBuild/artifact/artifacts/loci_tools.jar
3. download the ij_read_bio_formats.pro from Karsten Rodenacker's IDL Goodies
http://www.helmholtz-muenchen.de/ibb/homepage/karsten.rodena cker/IDL/_pro/ij_read_bio_formats.pro
4. modify ij_read_bio_formats.pro, insert SETENV right before objnew() like,
SETENV, 'IDLJAVAB_CONFIG=path\to\myjava\idljavabrc'
m = obj_new('IDLJavaObject$LOCI_FORMATS_IMAGEREADER','loci.forma ts.ImageReader')
5. copy idljavabrc from IDL82\resource\bridges\import\java to path\to\myjava\.
6. modify path\to\myjava\idljavabrc
JVM Classpath = path\to\myjava\loci_tools.jar;C:\Program Files\Exelis\IDL82\resource\bridges\import\java\jbexamples.j ar
also for logging
Log Location = path/to/myjava/LOG/
Bridge Logging = CONFIGFINE
7.copy the following and save as demo.pro
fn='path\to\data\test.tif'
a = ij_read_bio_formats(fn, info, /verbose, /raw)
help, info /str
end
8.start/restart idl workbench and run demo.pro, check error msgs and maybe logging info look like path\to\myjava\LOG\jb_logXXXXX.txt
That's it. The test.tif can be loaded into ImageJ with the same loci_tools.jar with any problem. I also tried jvm server from the ImageJ distro, same issue. Thank you so much for reading this.
On Monday, September 30, 2013 2:17:53 PM UTC-7, bio...@gmail.com wrote:
> Hi, Folks
>
>
>
> I have been trying to use bio-format via java bridge with IDL 8.2.3 under 64bit windows 7. And I am getting "Exception thrown java.lang.NullPointerException" during objnew() call to create the loci.format.ImageReader class. I also tried to enable logging and only get the following
>
>
>
> ##############jb_log15000.txt#################
>
> IDL-Java Bridge : May 3 2013 01:45:38
>
> Log Location : C:/Users/bp/idl_source/lab/bioformat/java/LOG/
>
> Bridge Logging : CONFIGFINE
>
> Config file : C:\Users\bp\idl_source\lab\bioformat\java\idljavabrc
>
> Exit Strategy : <null>
>
> Restart Bridge : FALSE
>
> EXCEPTION cJBExceptJavaException : NewObjectA
>
> ERR <IDL_JBCreateJavaObject return=0000000000000000
>
>
>
>
>
> The bio-format distribution of both 4.4.8 and 4.4.9 worked perfectly in ImageJ(Fiji). So I guess the problem is most likely the java bridge. But I don't know how to pursue further at this point. Any suggestions is highly appreciated!
>
>
>
> Thank you,
>
> BP
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