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

[Andreas Tille]

severity 859398 grave
thanks

As the bug reporter explains this bug needs to be considered
as grave.

On Mon, Apr 03, 2017 at 02:40:31PM +0200, Jonas D wrote:
> 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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