ImageJ (or Fiji) and JFreechart odd behavior?

[Colin Poczatek]

Hi all,

We have an IJ plugin that uses JFreechart.  To try to get more in line
with Fiji I tried to update our jar to match and test, we were one
version behind with jfree1.0.13 and jcommon1.0.16.  Now I seem to have
some odd behavior.  To explain:

- we have a class that extends ImagePlus, have several instances open
and listeners that synchronize which slice of the stack is displayed.

- with no JFreeshart plot open everything works as before.

- if a plot is open the images don't update.  I haven't fully debugged
this but it seems like the calls to ImagePlus.updateAndDraw() are
getting blocked.

- if the plot window is closed all the images then immediately update.

Basically I'm asking if anybody has noticed similar behavior since at
the moment I'm confused...

Thanks,
Collin


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[Jan Eglinger]

Hi Collin,

On 19.03.2013 6:11 PM, J Collin Poczatek wrote:

> We have an IJ plugin that uses JFreechart.  To try to get more in line
> with Fiji I tried to update our jar to match and test, we were one
> version behind with jfree1.0.13 and jcommon1.0.16.  Now I seem to have
> some odd behavior.  To explain:
>
> - we have a class that extends ImagePlus, have several instances open
> and listeners that synchronize which slice of the stack is displayed.
>
> - with no JFreeshart plot open everything works as before.
>
> - if a plot is open the images don't update.  I haven't fully debugged
> this but it seems like the calls to ImagePlus.updateAndDraw() are
> getting blocked.
>
> - if the plot window is closed all the images then immediately update.
>
> Basically I'm asking if anybody has noticed similar behavior since at
> the moment I'm confused...

Can you post the code of your plugin? I've tried with the JFreeChart
code from here:
http://fiji.sc/Scripting_toolbox#Plotting_charts_with_JFreeChart

running the Sync_Windows plugin in parallel:
http://fiji.sc/Sync_Windows

and changing brightness and contrast of some open images.
I did not observe any of the behaviour you are describing.

Jan

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[Colin Poczatek]

On 03/19/2013 01:40 PM, Jan Eglinger wrote:

> Hi Collin,
>
> On 19.03.2013 6:11 PM, J Collin Poczatek wrote:
>> We have an IJ plugin that uses JFreechart.  To try to get more in line
>> with Fiji I tried to update our jar to match and test, we were one
>> version behind with jfree1.0.13 and jcommon1.0.16.  Now I seem to have
>> some odd behavior.  To explain:
>>
>> - we have a class that extends ImagePlus, have several instances open
>> and listeners that synchronize which slice of the stack is displayed.
>>
>> - with no JFreeshart plot open everything works as before.
>>
>> - if a plot is open the images don't update.  I haven't fully debugged
>> this but it seems like the calls to ImagePlus.updateAndDraw() are
>> getting blocked.
>>
>> - if the plot window is closed all the images then immediately update.
>>
>> Basically I'm asking if anybody has noticed similar behavior since at
>> the moment I'm confused...
> Can you post the code of your plugin?

Thanks for the offer to look at it, but it's too big to post (a dozen or
so .java files).

> I've tried with the JFreeChart
> code from here:
> http://fiji.sc/Scripting_toolbox#Plotting_charts_with_JFreeChart
>
> running the Sync_Windows plugin in parallel:
> http://fiji.sc/Sync_Windows
>
> and changing brightness and contrast of some open images.
> I did not observe any of the behaviour you are describing.
I tried that too and also couldn't reproduce, but it's a little
different.  Running that javascript gives you a static plot that's been
rendered as an rgb image.

The way we're using JFreechart is crate a dynamic plot and display it
inside a JFrame.

I'm going to have to poke at this some more, and maybe see if I can
reproduce in a script separate from our plugin.  It just seems so odd to
me, cause it really behaves like the awt event queue is getting stalled
and then flushed when the plot closes...

Anyway, it's probably in our code, but I wanted to ask if anyone had
seen something similar.

Thanks,
Collin


> Jan
>
>



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[dscho]

Hi Collin,

On Tue, 19 Mar 2013, J Collin Poczatek wrote:

> Thanks for the offer to look at it, but it's too big to post (a dozen or
> so .java files).

There is always GitHub.

> Anyway, it's probably in our code, but I wanted to ask if anyone had
> seen something similar.

Yes, after Jan's analysis I am convinced of that. Feel free to post the
code if you want someone like me to have a look over it.

Ciao,
Johannes

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[Jan Eglinger]

Hi Collin,

On 19.03.2013 7:35 PM, J Collin Poczatek wrote:

> On 03/19/2013 01:40 PM, Jan Eglinger wrote:
>> On 19.03.2013 6:11 PM, J Collin Poczatek wrote:
>>> We have an IJ plugin that uses JFreechart.  To try to get more in line
>>> with Fiji I tried to update our jar to match and test, we were one
>>> version behind with jfree1.0.13 and jcommon1.0.16.  Now I seem to have
>>> some odd behavior.  To explain:
>>>
>>> - we have a class that extends ImagePlus, have several instances open
>>> and listeners that synchronize which slice of the stack is displayed.
>>>
>>> - with no JFreeshart plot open everything works as before.
>>>
>>> - if a plot is open the images don't update.  I haven't fully debugged
>>> this but it seems like the calls to ImagePlus.updateAndDraw() are
>>> getting blocked.
>>>
>>> - if the plot window is closed all the images then immediately update.
>>>
>>> Basically I'm asking if anybody has noticed similar behavior since at
>>> the moment I'm confused...
>> Can you post the code of your plugin?
> Thanks for the offer to look at it, but it's too big to post (a dozen or
> so .java files).
>
>> I've tried with the JFreeChart
>> code from here:
>> http://fiji.sc/Scripting_toolbox#Plotting_charts_with_JFreeChart
>>
>> running the Sync_Windows plugin in parallel:
>> http://fiji.sc/Sync_Windows
>>
>> and changing brightness and contrast of some open images.
>> I did not observe any of the behaviour you are describing.
> I tried that too and also couldn't reproduce, but it's a little
> different.  Running that javascript gives you a static plot that's been
> rendered as an rgb image.
>
> The way we're using JFreechart is crate a dynamic plot and display it
> inside a JFrame.

Have you tried using a PlugInFrame? It extends java.awt.Frame and you
can add an interactive/dynamic org.jfree.chart.ChartPanel to it.

I was using it in a small plugin, and do not see buggy behaviour.

> Anyway, it's probably in our code, but I wanted to ask if anyone had
> seen something similar.
>

As Johannes said, there's no sense in debugging without the source, so
if you post some code, we might be able to help.

Cheers,
Jan

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