integrating Tudor_DICOM_Pli

[Peter Gregson]

I want to include the Tudor_DICOM_Plugin as one of many in my ImageJ.  
However, the recommended method of installing Tudor_DICOM_Plugin  
requires using their starter.jar launcher and as a result I can either  
find my plugins or the Tudor_DICOM_Plugin but not both.  How do I  
install Tudor_DICOM_Plugin so that I can load my plugins as well?

Regards,
Peter

[Johannes Hermen]

The starter.jar only sets the classpath of ImageJ so that it contains all
jar files in the lib dir. If you put these libs in the classpath manually
you can allthough run the plugins without the starter.jar. We will
hopefully fix this issue in the next version.

Greets
        Johannes

-----------------------------------------------------------------
Johannes Hermen  -  Ingenieur de Recherche
[hidden email]
-----------------------------------------------------------------
CRP Henri Tudor  http://www.santec.tudor.lu
29, Avenue John F. Kennedy
L-1855 Luxembourg
-----------------------------------------------------------------

[Peter Gregson]

That is what I though, Johannes, but I tried it and it still failed.  
Is your ij.jar different from the ij.jar that is distributed with  
ImageJ?  There is an ij.jar file in your distribution as well.

Best regards,

Peter


On 18-Aug-08, at 3:04 AM, Johannes Hermen wrote:

> The starter.jar only sets the classpath of ImageJ so that it  
> contains all
> jar files in the lib dir. If you put these libs in the classpath  
> manually
> you can allthough run the plugins without the starter.jar. We will
> hopefully fix this issue in the next version.
>
> Greets
>        Johannes
>
> -----------------------------------------------------------------
> Johannes Hermen  -  Ingenieur de Recherche
> [hidden email]
> -----------------------------------------------------------------
> CRP Henri Tudor  http://www.santec.tudor.lu
> 29, Avenue John F. Kennedy
> L-1855 Luxembourg
> -----------------------------------------------------------------

[Peter Gregson]

I am still trying to get Tudor_DICOM_Plugin integrated with my ImageJ installation because I have a bunch of other plugins. I placed Tudor_DICOM_Plugin in the plugins directory of ImageJ and modified my startup script to include its jar files in the classpath.  However, when I start ImageJ with my script called "run", I get:


My "run" script is:

cd /AddIns/JavaApps/ImageJ
CLASSPATH=/AddIns/JavaApps/ImageJ/ij.jar
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/Image/Tudor_DICOM_Plugins
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/ImageJ/Tudor_DICOM_Plugin/lib/1_lu.tudor.santec/lu.tudor.santec.dicom.jar
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/ImageJ/Tudor_DICOM_Plugin/lib/1_lu.tudor.santec/lu.tudor.santec.i18n.jar
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/ImageJ/Tudor_DICOM_Plugin/lib/1_lu.tudor.santec/lu.tudor.santec.settings.jar
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/ImageJ/Tudor_DICOM_Plugin/lib/1_lu.tudor.santec/lu.tudor.santec.widgets.jar
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/ImageJ/Tudor_DICOM_Plugin/lib/com.jgoodies/forms/forms-1.0.6.jar
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/ImageJ/Tudor_DICOM_Plugin/lib/com.l2fprod.common/l2fprod-common-buttonbar.jar
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/ImageJ/Tudor_DICOM_Plugin/lib/dcm4che/dcm4che.jar
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/ImageJ/Tudor_DICOM_Plugin/lib/dcm4che/getopt.jar
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/ImageJ/Tudor_DICOM_Plugin/lib/dcm4che/log4j.jar
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/ImageJ/Tudor_DICOM_Plugin/lib/dcm4che/majix.jar
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/ImageJ/Tudor_DICOM_Plugin/lib/lu.tudor.santec.dicom.jar
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/ImageJ/Tudor_DICOM_Plugin/lib/lu.tudor.santec.i18n.jar
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/ImageJ/Tudor_DICOM_Plugin/lib/lu.tudor.santec.settings.jar
CLASSPATH=$CLASSPATH:/AddIns/JavaApps/ImageJ/Tudor_DICOM_Plugin/lib/lu.tudor.santec.widgets.jar
echo $CLASSPATH
java -cp $CLASSPATH -jar /AddIns/JavaApps/ImageJ/ij.jar

My directory structure is:



Note that the entire Tudor_DICOM_Plugin contents are installed as per instructions, except they are in the plugins directory, not ImageJ.

What am I doing wrong?

Regards,

Peter

Peter Gregson wrote

That is what I though, Johannes, but I tried it and it still failed.  
Is your ij.jar different from the ij.jar that is distributed with  
ImageJ?  There is an ij.jar file in your distribution as well.

Best regards,

Peter


On 18-Aug-08, at 3:04 AM, Johannes Hermen wrote:

> The starter.jar only sets the classpath of ImageJ so that it  
> contains all
> jar files in the lib dir. If you put these libs in the classpath  
> manually
> you can allthough run the plugins without the starter.jar. We will
> hopefully fix this issue in the next version.
>
> Greets
>        Johannes
>
> -----------------------------------------------------------------
> Johannes Hermen  -  Ingenieur de Recherche
> [e-mail]
> -----------------------------------------------------------------
> CRP Henri Tudor  http://www.santec.tudor.lu
> 29, Avenue John F. Kennedy
> L-1855 Luxembourg
> -----------------------------------------------------------------

[Johannes Hermen]

> java -cp $CLASSPATH -jar /AddIns/JavaApps/ImageJ/ij.jar

This will not work, as the Java VM does not use the "-cp" Variable if
started with "-jar"
Newer versions of ImageJ automatically load all jar-files that are placed
in the plugin dir. You can just place all the needed libs directly in the
plugins folder or in a direct  subfolder of it. Then ImageJ wil add them
to its classpath without hte need of a start script.

There will be a new Version of the DICOM Tools which will do that
automatically in November.

greets
             Johannes


-----------------------------------------------------------------
Johannes Hermen  -  Ingenieur de Recherche
[hidden email]
-----------------------------------------------------------------
CRP Henri Tudor  http://www.santec.tudor.lu
29, Avenue John F. Kennedy
L-1855 Luxembourg
-----------------------------------------------------------------

[Peter Gregson]

Thanks, Johannes.  I made the changes that you suggested so that now all jar files are in /AddIns/JavaApps/ImageJ/plugins/DICOM.  When I try to run it, I get:



My current directory structure is as follows:



This error happens whether I click on the ImageJ.app icon or execute "run" from terminal window.  "run" now contains just:

cd /AddIns/JavaApps/ImageJ
java -jar /AddIns/JavaApps/ImageJ/ij.jar

I think that I have moved all the jar files as you suggested.  How can I get this working?

Best regards,
Peter

Johannes Hermen wrote

> java -cp $CLASSPATH -jar /AddIns/JavaApps/ImageJ/ij.jar

This will not work, as the Java VM does not use the "-cp" Variable if
started with "-jar"
Newer versions of ImageJ automatically load all jar-files that are placed
in the plugin dir. You can just place all the needed libs directly in the
plugins folder or in a direct  subfolder of it. Then ImageJ wil add them
to its classpath without hte need of a start script.

There will be a new Version of the DICOM Tools which will do that
automatically in November.

greets
             Johannes


-----------------------------------------------------------------
Johannes Hermen  -  Ingenieur de Recherche
[e-mail]
-----------------------------------------------------------------
CRP Henri Tudor  http://www.santec.tudor.lu
29, Avenue John F. Kennedy
L-1855 Luxembourg
-----------------------------------------------------------------