Call multithreaded plugin from another plugin

[Michael Doube]

Hi all

I have a plugin that I've multithreaded (Purify) that I'd like to call
from another plugin.  I've already reduced the code in Purify's run()
method to a call to show a dialog ( showDialog() ) and a call to a
method, purify(), that calls the rest of the plugin using the variables
returned by showDialog().  Purify works fine when I run it directly from
the Plugins menu, but when I call it from another plugin, e.g.

Purify p = new Purify();
p.purify(important, variables).show(); //p.purify returns an ImagePlus

It hangs in the middle of part of Purify that is multithreaded.  It runs
properly when I run it with only 1 chunk (i.e. not multithreaded).

The multithreading is done in a subclass, as in Bob Dougherty's
LocalThickness, and I wonder if there is something important that I am
missing when making the call to Purify's methods from another class.

The code is here:
http://github.com/mdoube/BoneJ/blob/master/src/org/doube/bonej/Purify.java

Cheers

Mike

[Ignacio Arganda-Carreras]

Hi Mike,

I think the fields on ConnectStructuresThread class should all be
"final" to make sure you are not accessing the same memory from
different threads.

You have some examples of multithreading  in bUnwarpJ code if you want
to have a look.

Good luck!

ignacio

On Tue, Sep 22, 2009 at 11:33 AM, Michael Doube <[hidden email]> wrote:

>
> Hi all
>
> I have a plugin that I've multithreaded (Purify) that I'd like to call from another plugin.  I've already reduced the code in Purify's run() method to a call to show a dialog ( showDialog() ) and a call to a method, purify(), that calls the rest of the plugin using the variables returned by showDialog().  Purify works fine when I run it directly from the Plugins menu, but when I call it from another plugin, e.g.
>
> Purify p = new Purify();
> p.purify(important, variables).show(); //p.purify returns an ImagePlus
>
> It hangs in the middle of part of Purify that is multithreaded.  It runs properly when I run it with only 1 chunk (i.e. not multithreaded).
>
> The multithreading is done in a subclass, as in Bob Dougherty's LocalThickness, and I wonder if there is something important that I am missing when making the call to Purify's methods from another class.
>
> The code is here:
> http://github.com/mdoube/BoneJ/blob/master/src/org/doube/bonej/Purify.java
>
> Cheers
>
> Mike

--
Ignacio Arganda-Carreras, Ph.D.
Institute of Neuroinformatics
Uni/ETH Zurich
Winterthurerstrasse 190
Bau 55
Zurich 8057
[phone]

Website: http://bioweb.cnb.csic.es/~iarganda/

[Albert Cardona-2]

Michael Doube wrote:

> Hi all
>
> I have a plugin that I've multithreaded (Purify) that I'd like to call
> from another plugin.  I've already reduced the code in Purify's run()
> method to a call to show a dialog ( showDialog() ) and a call to a
> method, purify(), that calls the rest of the plugin using the variables
> returned by showDialog().  Purify works fine when I run it directly from
> the Plugins menu, but when I call it from another plugin, e.g.
>
> Purify p = new Purify();
> p.purify(important, variables).show(); //p.purify returns an ImagePlus
>
> It hangs in the middle of part of Purify that is multithreaded.  It runs
> properly when I run it with only 1 chunk (i.e. not multithreaded).

If there is an Exception stack trace, please print it here.

If there isn't (thread lock up), launch the JVM from a command line and,
  when it hangs, push control+\  (control backslash) on the command line,
and paste us here the entire set of stack traces (one per thread).

Albert

[Michael Schmid]

Hi Michael,

it seems that you are using global variables (class variables) that  
are not set if you don't call showDialog. E.g., getChunkRanges uses  
slicesPerChunk; but there are more.

Michael
________________________________________________________________

On 22 Sep 2009, at 11:33, Michael Doube wrote:

> Hi all
>
> I have a plugin that I've multithreaded (Purify) that I'd like to  
> call from another plugin.  I've already reduced the code in  
> Purify's run() method to a call to show a dialog ( showDialog() )  
> and a call to a method, purify(), that calls the rest of the plugin  
> using the variables returned by showDialog().  Purify works fine  
> when I run it directly from the Plugins menu, but when I call it  
> from another plugin, e.g.
>
> Purify p = new Purify();
> p.purify(important, variables).show(); //p.purify returns an ImagePlus
>
> It hangs in the middle of part of Purify that is multithreaded.  It  
> runs properly when I run it with only 1 chunk (i.e. not  
> multithreaded).
>
> The multithreading is done in a subclass, as in Bob Dougherty's  
> LocalThickness, and I wonder if there is something important that I  
> am missing when making the call to Purify's methods from another  
> class.
>
> The code is here:
> http://github.com/mdoube/BoneJ/blob/master/src/org/doube/bonej/ 
> Purify.java
>
> Cheers
>
> Mike

[Michael Doube]

Michael, Wayne, Ignacio, Albert

I fixed my code with a combination of your suggestions, and following
the Fiji design guidelines,

http://pacific.mpi-cbg.de/wiki/index.php/PlugIn_Design_Guidelines

Mike

Michael Schmid wrote:

> Hi Michael,
>
> it seems that you are using global variables (class variables) that  
> are not set if you don't call showDialog. E.g., getChunkRanges uses  
> slicesPerChunk; but there are more.
>
> Michael
> ________________________________________________________________
>
> On 22 Sep 2009, at 11:33, Michael Doube wrote:
>
>  
>> Hi all
>>
>> I have a plugin that I've multithreaded (Purify) that I'd like to  
>> call from another plugin.  I've already reduced the code in  
>> Purify's run() method to a call to show a dialog ( showDialog() )  
>> and a call to a method, purify(), that calls the rest of the plugin  
>> using the variables returned by showDialog().  Purify works fine  
>> when I run it directly from the Plugins menu, but when I call it  
>> from another plugin, e.g.
>>
>> Purify p = new Purify();
>> p.purify(important, variables).show(); //p.purify returns an ImagePlus
>>
>> It hangs in the middle of part of Purify that is multithreaded.  It  
>> runs properly when I run it with only 1 chunk (i.e. not  
>> multithreaded).
>>
>> The multithreading is done in a subclass, as in Bob Dougherty's  
>> LocalThickness, and I wonder if there is something important that I  
>> am missing when making the call to Purify's methods from another  
>> class.
>>
>> The code is here:
>> http://github.com/mdoube/BoneJ/blob/master/src/org/doube/bonej/ 
>> Purify.java
>>
>> Cheers
>>
>> Mike
>>    

--
Dr Michael Doube  BPhil BVSc PhD MRCVS
Research Associate
Department of Bioengineering
Imperial College London
South Kensington Campus
London  SW7 2AZ
United Kingdom