http://imagej.273.s1.nabble.com/imagej-and-Java-1-8-tp5015143p5015176.html
makes a reproducible difference. If it exists, then after running this
> Thanks Aryeh!
>
> >How are hard references created?
>
> So first let me apologize for dragging you into the world of
> references. It is not a happy place and certainly not something a user
> or biologist should have to worry about, as it gets into the inner
> workings of Java itself.
>
> There's a nice succinct description of the different references here[1].
>
> Basically when an object is created it gets a "strong" by default, and
> you have to use special Java classes to get the other reference types.
> You get memory leaks when those strong references persist longer than
> expected (for example because they were created by something
> fundamental to the program).
>
> The way to fix the problem varies based on the actual cause - in your
> case it could be a bug in Jython itself.
>
> I'll look at your script and report back!
>
> Thanks again,
> Mark
>
> [1]
>
https://www.rallydev.com/blog/engineering/java-references-strong-soft-weak-phantom>
>
> On Tue, Dec 8, 2015 at 10:33 AM, Aryeh Weiss <
[hidden email]
> <mailto:
[hidden email]>> wrote:
>
> Hi Mark
>
> Thank you for this quick reply.
> I am replying off-list so that I can attach the script.
>
> On 08/12/2015 5:07 PM, Mark Hiner wrote:
>> Hi Aryeh!
>>
>> >I hope that this is useful.
>>
>> Yep this is exactly what I needed and your thoroughness is
>> greatly appreciated. :)
>>
>> I started with heapdump-144955328636 and it was immediately clear
>> that something on the python side is keeping hard references to
>> your images. It looks like they are being stored in a
>> ConcurrentHashMap which is not cleaned up when your script ends.
>>
>> So it looks like a bug in the Python script you're using. I put
>> up some screen captures[1] of the reference path that's keeping
>> your objects alive, along with a brief interpretation. The
>> variable names are distinct so I'm hoping it will be obvious
>> where in your script they are being mapped. Ideally I would
>> suggest caching weak references on the python side if that's an
>> option, or possibly clearing the cache at the end of the script.
>>
> I do not have any variable named snapshotPixels (or rLUT1, rLUT2,
> etc), so I assume that these are variables internal to some plugin
> that is used (or perhaps internal to IJ.
>
> Some very basic questions:
> How are hard references created?
> Is there a way at the end of a script to tell it to clear all such
> reference?
>
>> If it's not clear how to fix the script and you'd like more eyes
>> on it, share it here - happy to have a look! :) Also happy to
>> give more info on the heap dump analysis if anything's unclear there.
>>
>
> I attached the script -- it is not well written (to say the very
> least), as I am new at muddling my way through the API. The most
> recent addition to it is the mouse listener which I added to allow
> the user to select three points near the end of the script.
>
> Best regards
> --aryeh
>
>> If anyone else is interested in looking at the heap dumps I
>> personally recommend the Eclipse Memory Analyzer plugin[2].
>>
>> Best,
>> Mark
>>
>> [1]
https://gist.github.com/hinerm/727453aab0837246367e>> [2]
https://eclipse.org/mat/downloads.php>>
>> On Tue, Dec 8, 2015 at 2:25 AM, Aryeh Weiss <
[hidden email]
>> <mailto:
[hidden email]>> wrote:
>>
>>
>> Hi Mark
>>
>> On 07/12/2015 11:04 PM, Mark Hiner wrote:
>>> Hi Aryeh,
>>>
>>> On Mon, Dec 7, 2015 at 11:46 AM, Aryeh Weiss
>>> <
[hidden email] <mailto:
[hidden email]>> wrote:
>>>
>>> Thanks for this information. I decided to run IJ, do a
>>> heap dump before running a script that opens a few
>>> 1.3Gpixel images, then run it after, then close the
>>> images and get a heap dump when the images have been
>>> closed but the memory is not freed (which is reproducible).
>>>
>>>
>>> This sounds like the perfect set of information!
>>>
>>> > In order to send it to you, I will probably need to send
>>> it to an FTP server (like I have done with bio-formats. DO
>>> you have a server to which I can send the dumps?
>>>
>>> Actually you should be able to use the Upload Sample
>>> Image[1] command to send the zip. If that doesn't work for
>>> you let me know and I can send FTP credentails.
>>>
>>
>> I uploaded a set of heap dumps using Upload Sample Image as
>> you suggested.
>> They are:
>> heapdump-1449551945772 -- made immediately after launching
>> Fiji. Small, as expected.
>> heapdump-1449552198991 -- made immediately after running my
>> python script. Three large image are open.
>> heapdump-1449552667004 -- made after closing those three
>> large images and double clicking in the Fiji window
>> a few times to run the garbage collector
>> heapdump-1449553044705 -- made after running the script a
>> second time, during which Fiji ran out of memory.
>> Two large images are open.
>> heapdump-1449553286368 -- made after closing those two
>> windows and garbage collecting.
>> As expected, memory was not freed.
>>
>> The large images are a bit under 1Gpixel, 8-bit images.
>>
>> I hope that this is useful.
>> Thanks for your efforts.
>> --aryeh
>>