Increasing running times - Versatile Wand plugin

[Avital Steinberg]

Hi,
I'm running an imageJ macro that calls the Versatile Wand plugin and uses
it 10 times per image. I manually open an image such as the attached image,
then run the following code:

run("Gaussian Blur...", "sigma=2");
WANDS           = newArray(75, 10, 50, 20, 30,35, 76,90,105,0);
run("Set Scale...", "global");
start = getTime();
for(wandValue=0; wandValue < WANDS.length-1; wandValue++){
    run("Versatile Wand", "value="+WANDS[wandValue]+" color=-100
gradient="+10+" connectedness=4-connected x="+780+" y="+780+" do");
}
end = getTime();
itTook = (end - start)/1000;
print("Running time: " + itTook);

And then manually close the image. The first time I ran it, it took 11.028
seconds, the second time: 22.782 seconds, the third time: 38.631, and the
fourth time - it ran so slowly that I had to kill it. It always happens
like this and I have to restart Fiji in order to be able to continue
running my macro on additional images.

What might the problem be? (I'm running it on a mac 10.9.5)

Thank you,
Avital

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[ctrueden]

Hi Avital,

> the fourth time - it ran so slowly that I had to kill it.

You can do a full thread dump to see what's going on when ImageJ gets slow.

  http://imagej.net/Debugging#Debugging_JVM_hangs

Would probably shed some light on what ImageJ is doing that is taking so
long.

Regards,
Curtis

On Fri, Apr 10, 2015 at 11:24 AM, Avital Steinberg <
[hidden email]> wrote:

> Hi,
> I'm running an imageJ macro that calls the Versatile Wand plugin and uses
> it 10 times per image. I manually open an image such as the attached image,
> then run the following code:
>
> run("Gaussian Blur...", "sigma=2");
> WANDS           = newArray(75, 10, 50, 20, 30,35, 76,90,105,0);
> run("Set Scale...", "global");
> start = getTime();
> for(wandValue=0; wandValue < WANDS.length-1; wandValue++){
>     run("Versatile Wand", "value="+WANDS[wandValue]+" color=-100
> gradient="+10+" connectedness=4-connected x="+780+" y="+780+" do");
> }
> end = getTime();
> itTook = (end - start)/1000;
> print("Running time: " + itTook);
>
> And then manually close the image. The first time I ran it, it took 11.028
> seconds, the second time: 22.782 seconds, the third time: 38.631, and the
> fourth time - it ran so slowly that I had to kill it. It always happens
> like this and I have to restart Fiji in order to be able to continue
> running my macro on additional images.
>
> What might the problem be? (I'm running it on a mac 10.9.5)
>
> Thank you,
> Avital
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Michael Schmid]

Hi Avital,

hmm, I can't reproduce this. With the image in your attachment, I always get about 5.5 to 6 seconds on my computer, independent on how often I run it.
CPU: 2.4 GHz Core2 Duo; plain ImageJ 1.49q, but that should not matter; 64-bit Java 1.6.0_65.

Do you get the same result if you take the JPG from the list? JPG is a lossy compression, so it changes the pixel values. Also it is only 8 bits and does not keep the calibration, if any (the Versatile Wand uses the pixel value calibration).

The speed of the Versatile Wand with gradient tolerance strongly depends on the image data (it uses a very simple queue-based flood fill algorithm), so you may experience some change in computing time with successive smoothing of the image. I tried converting the image to 16 bits and multiplying the image values by various numbers, and saw that it becomes slower for some values. The maximum I have ever seen was 25 seconds for the 10 'WANDS' selections. This was with to a very "fractal" selection. It never seemed to hang. You should also see the progress bar in the ImageJ panel running, even if it is slow.

Michael
________________________________________________________________
On Apr 10, 2015, at 18:24, Avital Steinberg wrote:

> Hi,
> I'm running an imageJ macro that calls the Versatile Wand plugin and uses
> it 10 times per image. I manually open an image such as the attached image,
> then run the following code:
>
> run("Gaussian Blur...", "sigma=2");
> WANDS           = newArray(75, 10, 50, 20, 30,35, 76,90,105,0);
> run("Set Scale...", "global");
> start = getTime();
> for(wandValue=0; wandValue < WANDS.length-1; wandValue++){
>    run("Versatile Wand", "value="+WANDS[wandValue]+" color=-100
> gradient="+10+" connectedness=4-connected x="+780+" y="+780+" do");
> }
> end = getTime();
> itTook = (end - start)/1000;
> print("Running time: " + itTook);
>
> And then manually close the image. The first time I ran it, it took 11.028
> seconds, the second time: 22.782 seconds, the third time: 38.631, and the
> fourth time - it ran so slowly that I had to kill it. It always happens
> like this and I have to restart Fiji in order to be able to continue
> running my macro on additional images.
>
> What might the problem be? (I'm running it on a mac 10.9.5)
>
> Thank you,
> Avital

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[Avital Steinberg]

Thank you, Curtis and Michael for your answers. I emailed Michael to
continue the discussion, since he wrote the Versatile Wand.

Best Regards,
Avital

On Fri, Apr 10, 2015 at 8:07 PM, Michael Schmid <[hidden email]>
wrote:

> Hi Avital,
>
> hmm, I can't reproduce this. With the image in your attachment, I always
> get about 5.5 to 6 seconds on my computer, independent on how often I run
> it.
> CPU: 2.4 GHz Core2 Duo; plain ImageJ 1.49q, but that should not matter;
> 64-bit Java 1.6.0_65.
>
> Do you get the same result if you take the JPG from the list? JPG is a
> lossy compression, so it changes the pixel values. Also it is only 8 bits
> and does not keep the calibration, if any (the Versatile Wand uses the
> pixel value calibration).
>
> The speed of the Versatile Wand with gradient tolerance strongly depends
> on the image data (it uses a very simple queue-based flood fill algorithm),
> so you may experience some change in computing time with successive
> smoothing of the image. I tried converting the image to 16 bits and
> multiplying the image values by various numbers, and saw that it becomes
> slower for some values. The maximum I have ever seen was 25 seconds for the
> 10 'WANDS' selections. This was with to a very "fractal" selection. It
> never seemed to hang. You should also see the progress bar in the ImageJ
> panel running, even if it is slow.
>
> Michael
> ________________________________________________________________
> On Apr 10, 2015, at 18:24, Avital Steinberg wrote:
>
> > Hi,
> > I'm running an imageJ macro that calls the Versatile Wand plugin and uses
> > it 10 times per image. I manually open an image such as the attached
> image,
> > then run the following code:
> >
> > run("Gaussian Blur...", "sigma=2");
> > WANDS           = newArray(75, 10, 50, 20, 30,35, 76,90,105,0);
> > run("Set Scale...", "global");
> > start = getTime();
> > for(wandValue=0; wandValue < WANDS.length-1; wandValue++){
> >    run("Versatile Wand", "value="+WANDS[wandValue]+" color=-100
> > gradient="+10+" connectedness=4-connected x="+780+" y="+780+" do");
> > }
> > end = getTime();
> > itTook = (end - start)/1000;
> > print("Running time: " + itTook);
> >
> > And then manually close the image. The first time I ran it, it took
> 11.028
> > seconds, the second time: 22.782 seconds, the third time: 38.631, and the
> > fourth time - it ran so slowly that I had to kill it. It always happens
> > like this and I have to restart Fiji in order to be able to continue
> > running my macro on additional images.
> >
> > What might the problem be? (I'm running it on a mac 10.9.5)
> >
> > Thank you,
> > Avital
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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