Morphology collection update & new IJ_Robot plugin

[Gabriel Landini]

Hi,
I have updated the morphology plugin collection.
Now BinaryFilterReconstruct and BinaryReconstruct use an alternative algorithm
that is considerably faster.
(For those insterested, instead of repeated dilations of the seed inside the
mask until idempotence, it floodfills [8 neighbours] the mask from the seed
pixels).
New macro example of hole filling using binary reconstruction.
New macro to count holes, particles and calculate the Euler number of a binary
image.

To run those you need IJ 1.37e.

I also uploaded the IJ_Robot plugin and an example (many thanks to all the
people who tested it).

Downloads and instructions here:

http://www.dentistry.bham.ac.uk/landinig/software/software.html


Please report any problems.
Cheers,

Gabriel

[Robert Baer]

For some time now it seems that the start-up time for imageJ is considerably
longer than it used to be when I first started using it.  I currently have
the WCIF version installed (at 1.37a), but the same seems to be true of the
standard ImageJ download.   For example, after double clicking on the
desktop icon for imageJ just now, it took about 45 seconds before the ImageJ
main panel appeared.  This example is from a 1.4 GHz Pentium with 768 Mb of
RAM running Windows 2000.  On faster machines this start-up penalty does not
disappear although I have not timed it to see exactly how long it takes.

I'm not certain if this is related to the Java virtual machine (version
1.5.0_06) or something else.  Are there some environmental variables that I
should check or something I could do to the configuration file to speed
start-up?  Should Java be pre-started in some manner?  Even if this is just
the norm and there is nothing I can do, I'd still like to understand what's
happening.

Thanks for any insights,

Rob
____________________________
Robert W. Baer, Ph.D.
Associate Professor
Department of Physiology
A. T. Still University of Health Science
800 W. Jefferson St.
Kirksville, MO 63501-1497 USA

[Hemerson Pistori]

Dear Rob,

> ...On faster machines this start-up penalty does not
> disappear although I have not timed it to see exactly how long it takes.

   It takes me less than 2 seconds to start ImageJ up on a 3.1 Ghz Dual
Pentium with 1Gb RAM running Fedore Core 5. I'm using ImageJ 1.37i (but
older versions used to load fast as well). My virtual machine is SUN's
jdk1.5.0_06.

PS: The start up takes no more than 4 seconds on a Compaq nc6120 Laptop
(also running Linux FC5 on a Pentium ).

Best Regards,

Hemerson Pistori
http://www.ec.ucdb.br/~pistori

>
> I'm not certain if this is related to the Java virtual machine (version
> 1.5.0_06) or something else.  Are there some environmental variables that I
> should check or something I could do to the configuration file to speed
> start-up?  Should Java be pre-started in some manner?  Even if this is just
> the norm and there is nothing I can do, I'd still like to understand what's
> happening.
>
> Thanks for any insights,
>
> Rob
> ____________________________
> Robert W. Baer, Ph.D.
> Associate Professor
> Department of Physiology
> A. T. Still University of Health Science
> 800 W. Jefferson St.
> Kirksville, MO 63501-1497 USA

[dscho]

Hi,

On Thu, 29 Jun 2006, Robert Baer wrote:

> For some time now it seems that the start-up time for imageJ is considerably
> longer than it used to be when I first started using it.  I currently have
> the WCIF version installed (at 1.37a), but the same seems to be true of the
> standard ImageJ download.   For example, after double clicking on the
> desktop icon for imageJ just now, it took about 45 seconds before the ImageJ
> main panel appeared.  This example is from a 1.4 GHz Pentium with 768 Mb of
> RAM running Windows 2000.  On faster machines this start-up penalty does not
> disappear although I have not timed it to see exactly how long it takes.

This sooo sounds like an overzealous Antivirus.

Ciao,
Dscho

[Robert Baer]

>> the start-up time for imageJ is considerably
> > longer than it used to be
-- snip --
> This sooo sounds like an overzealous Antivirus.
>
> Ciao,
> Dscho

Most excellent call !!!!  I uninstalled my antivirus program and ImageJ
startup time was decidedly below 3 seconds MAX.  Allowed the virus program
to repair itself and the problem is back.  Now all I have to do is figure
out how to enforce peaceful co-existance between the virus program and
ImageJ!  This probably means involving IT since I seem to not be able to
adjust many aspects of the virus program's properties.

FWIW my antivirus is McAfee VirusScan Enterprise 8.0.0 running from a Novell
Network environment.  Thanks, Dscho, for the insight!.

Rob

____________________________
Robert W. Baer, Ph.D.
Associate Professor
Department of Physiology
A. T. Still University of Health Science
800 W. Jefferson St.
Kirksville, MO 63501-1497 USA

[dscho]

Hi,

On Thu, 29 Jun 2006, Robert Baer wrote:

> > This sooo sounds like an overzealous Antivirus.
>
> Thanks, Dscho, for the insight!.

You're welcome!

Although I have to say it was not that difficult for me to tell: I spend
my days at the office (where people make me use Windows... pfffh) cursing
loud and long about how slow the darn box is, just because Microsoft
spends way more money on lawyers and PR than on developers.

Ciao,
Dscho