[Debian-med-packaging] Bug#859398: imagej: default memory "allowance" too little

[Jonas D]

This issue affects all users working on large series of 2D images
or 3D volumetric data. This is typical in medical imaging,
and handling of such datasets is a core functionality
of ImageJ (cf. DICOM support, the Image>Stacks menu,
or the Process->Filters-> * 3D functions).
3D datasets typically range from 0.5 to 10 GB.

Given the simple solution, i would suggest to fix it within
the stable release, although i cannot oversee the
implications this might have on the Debian release process.

For future releases, i suggest to consider the "Fiji"
ImageJ (www.fiji.sc) distribution which packages a large
amount of available (and useful) ImageJ plugins and further
does not impose artificial memory limitations.


Kind regards,
Jonas


On Mon, Apr 3, 2017 at 10:14 AM, Jonas D <bugpublic at googlemail.com> wrote:

> Package: imagej
> Version: 1.51i+dfsg-1
> Severity: normal
> Tags: lfs patch
>
> Dear Maintainer,
>
>
> ImageJ limits the amount of total RAM it (the JVM) will allocate
> when loading images etc. On Linux systems, this amount is
> defined on startup (within the /usr/bin/imagej shellscript) and
> (other than on Windows) cannot be changed during runtime.
>
> The amount is currently fixed to 500MB, which (artificially)
> prohibits loading of larger 3D volume datasets as typical
> in tomographic imaging applications.
>
> I propose to change the default setting to 4000MB, which is
> the maximum possible value as stated in the imagej shellscript.
>
> A corresponding patch is attached.
>
>
> Kind regards,
> Jonas
>
>
>
>
>
>
>
> -- System Information:
> Debian Release: 9.0
>   APT prefers testing
>   APT policy: (500, 'testing'), (500, 'stable')
> Architecture: amd64 (x86_64)
> Foreign Architectures: i386
>
> Kernel: Linux 4.8.0-2-amd64 (SMP w/8 CPU cores)
> Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
>
> Versions of packages imagej depends on:
> ii  default-jre  2:1.8-58
>
> imagej recommends no packages.
>
> imagej suggests no packages.
>
> -- no debconf information
>
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