Re: Problems using Versatile wand - am I using it wrong?

[Michael Schmid]

Hi Avital,

strange. Without changing the jpeg to 16 bits, I always get about 5-6 seconds (the first run may be slightly slower, 7 sec). No change even after 10 times.
Does memory usage increase significantly? (click in the status line a few times).
After running the macro 10 times, I see about 11 MB used, which is about the same as if I open the image and run one Gaussian Blur.

Do you have the latest Versatile Wand version?
  http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start
(anyhow, I don't remember an issue like this with previous verions)

Michael
________________________________________________________________
On Apr 10, 2015, at 19:28, Avital Steinberg wrote:

> Hi Michael,
> Thanks for your answer - with the jpg image that I attached, it got stuck. This only happens after I run it a few times. (without closing Fiji) I used the input image exactly as is. (as .jpg, not as tif, and it is an 8-bit image)
>
> Is the way I'm using Versatile Wand wrong? When you ran Versatile Wand with the image I attached to the question in the list, did you change it to a 16 bit tif first?
>
> Thank you,
> Avital

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[Michael Schmid]

Hi Avital,

this looks like a memory leak - I have never seen this with plain ImageJ
and Java 1.5 or 1.6.
As you are using Fiji - are any ImageJ2 features enabled in Edit>Options?
E.g. "Enable ImageJ2 data structures"?

If so, it might be a problem of ImageJ2; then try with disabling all
ImageJ2 features.
Otherwise it might also be a problem with the Java version - see here for
how to switch to Java 6:
  http://fiji.sc/Frequently_Asked_Questions#How_do_I_set_up_Java_6_on_OS_X.3F

Michael
__________________________________________________________________


On Fri, April 10, 2015 20:00, Avital Steinberg wrote:

> Hi Michael,
> I checked the memory. The first time I ran it, it was 39 MB, the second
> time 64 MB, the third time 78 MB, the fourth time 181 MB (and it took
> 41.65
> seconds), and when it really got stuck, it took 357 MB of memory.
>
> I'm running a new version of Versatile Wand - I don't see the version
> number, but there's a list of bug fixes and the last one is:
>
> Version 1.15, Michael Schmid, 2014-Jul-30:
>
> Thank you,
> Avital
>
> On Fri, Apr 10, 2015 at 8:38 PM, Michael Schmid <[hidden email]>
> wrote:
>
>> Hi Avital,
>>
>> strange. Without changing the jpeg to 16 bits, I always get about 5-6
>> seconds (the first run may be slightly slower, 7 sec). No change even
>> after
>> 10 times.
>> Does memory usage increase significantly? (click in the status line a
>> few
>> times).
>> After running the macro 10 times, I see about 11 MB used, which is about
>> the same as if I open the image and run one Gaussian Blur.
>>
>> Do you have the latest Versatile Wand version?
>>
>> http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start
>> (anyhow, I don't remember an issue like this with previous verions)
>>
>> Michael
>> ________________________________________________________________
>> On Apr 10, 2015, at 19:28, Avital Steinberg wrote:
>>
>> > Hi Michael,
>> > Thanks for your answer - with the jpg image that I attached, it got
>> stuck. This only happens after I run it a few times. (without closing
>> Fiji)
>> I used the input image exactly as is. (as .jpg, not as tif, and it is an
>> 8-bit image)
>> >
>> > Is the way I'm using Versatile Wand wrong? When you ran Versatile Wand
>> with the image I attached to the question in the list, did you change it
>> to
>> a 16 bit tif first?
>> >
>> > Thank you,
>> > Avital
>>
>>
>

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