BAR tools "Find peaks" crashes on latest Fiji

[lechristophe]

Hi Tiago and the ImageJ listers,

I wanted to try the BAR tool "Find Peaks", so I installed BAR tools from
its update site in Fiji. When I open the AuPbSn example image, draw a
straight line, make a profile plot using cmd+K, then launch BAR>Data
Analysis>Find Peaks, I get an exception (see end of post).

Did I do something wrong or is there a problem here?

Thanks for the help,

Christophe


(Fiji Is Just) ImageJ 2.0.0-rc-25/1.49m; Java 1.6.0_65 [64-bit]; Mac OS X
10.10.2; 88MB of 5987MB (1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException:
java.lang.NullPointerException
at
net.imagej.legacy.DefaultLegacyService.runLegacyCompatibleCommand(DefaultLegacyService.java:271)
at
net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:160)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:695)
Caused by: java.util.concurrent.ExecutionException:
java.lang.NullPointerException
at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
at java.util.concurrent.FutureTask.get(FutureTask.java:83)
at
net.imagej.legacy.DefaultLegacyService.runLegacyCompatibleCommand(DefaultLegacyService.java:267)
... 5 more
Caused by: java.lang.NullPointerException
at
net.imagej.legacy.translate.AbstractDisplayCreator.getDataset(AbstractDisplayCreator.java:76)
at
net.imagej.legacy.translate.GrayDisplayCreator.grayCase(GrayDisplayCreator.java:159)
at
net.imagej.legacy.translate.GrayDisplayCreator.makeDisplay(GrayDisplayCreator.java:129)
at
net.imagej.legacy.translate.AbstractDisplayCreator.createDisplay(AbstractDisplayCreator.java:63)
at
net.imagej.legacy.translate.DefaultImageTranslator.createDisplay(DefaultImageTranslator.java:100)
at
net.imagej.legacy.translate.DefaultImageTranslator.createDisplay(DefaultImageTranslator.java:84)
at
net.imagej.legacy.LegacyImageMap.registerLegacyImage(LegacyImageMap.java:271)
at
net.imagej.legacy.display.LegacyImageDisplayService.getActiveImageDisplay(LegacyImageDisplayService.java:119)
at
net.imagej.display.ActiveImagePreprocessor.process(ActiveImagePreprocessor.java:88)
at org.scijava.module.ModuleRunner.preProcess(ModuleRunner.java:104)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:156)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
at
org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
... 1 more

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[Tiago Ferreira-2]

Hi Christophe,

On Feb 28, 2015, at 09:56, Christophe Leterrier <[hidden email]> wrote:
> When I open the AuPbSn example image, draw a straight line, make a profile plot using cmd+K,
> then launch BAR>Data Analysis>Find Peaks, I get an exception (see end of post).


Not really sure what is going on. But it does not seem to be BAR specific.
If I had to guess, I'd say it is related by the recent Fiji update.

It seems the Exception is only triggered by the first run. Launching Find Peaks afterwards seems
to work as expected. So you could the following workarounds:

1) After you get the error, close the Exception window and re-run BAR>Data Analysis>Find Peaks

2) Running the script from the Script Editor directly also seems to work:
  a) Open the Find_Peaks.bsh file by holding shift while selecting BAR>Data Analysis>Find Peaks
     (This will open the script in the script editor)
  b) Then run the script from the Script Editor (by pressing run, or Cmd/Ctrl R).
     (Also here, It seems one has to press "Run" twice to successfully launch the script)


I do not have much time to look into it, but it seems really to be triggered on 1st run only.
I will try to look into it ASA as I get some more time, meanwhile do let me know if the above
workarounds work for you.

thanks,
-tiago
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[ctrueden]

Hi Christophe, Tiago & everyone,

> If I had to guess, I'd say it is related by the recent Fiji update.

Yes, there were several reports of this issue. A fix has been uploaded; run
Help > Update... to receive it.

Regards,
Curtis

On Sat, Feb 28, 2015 at 10:30 AM, Tiago Ferreira <
[hidden email]> wrote:

> Hi Christophe,
>
> On Feb 28, 2015, at 09:56, Christophe Leterrier <
> [hidden email]> wrote:
> > When I open the AuPbSn example image, draw a straight line, make a
> profile plot using cmd+K,
> > then launch BAR>Data Analysis>Find Peaks, I get an exception (see end of
> post).
>
>
> Not really sure what is going on. But it does not seem to be BAR specific.
> If I had to guess, I'd say it is related by the recent Fiji update.
>
> It seems the Exception is only triggered by the first run. Launching Find
> Peaks afterwards seems
> to work as expected. So you could the following workarounds:
>
> 1) After you get the error, close the Exception window and re-run BAR>Data
> Analysis>Find Peaks
>
> 2) Running the script from the Script Editor directly also seems to work:
>   a) Open the Find_Peaks.bsh file by holding shift while selecting
> BAR>Data Analysis>Find Peaks
>      (This will open the script in the script editor)
>   b) Then run the script from the Script Editor (by pressing run, or
> Cmd/Ctrl R).
>      (Also here, It seems one has to press "Run" twice to successfully
> launch the script)
>
>
> I do not have much time to look into it, but it seems really to be
> triggered on 1st run only.
> I will try to look into it ASA as I get some more time, meanwhile do let
> me know if the above
> workarounds work for you.
>
> thanks,
> -tiago
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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