Posted by
Divakar Ramachandran-2 on
Mar 25, 2011; 9:51pm
URL: http://imagej.273.s1.nabble.com/ImageJ-under-Ubuntu-10-04-64-bit-tp3685262p3685265.html
On Tuesday 22 March 2011 08:34 PM, Johannes Schindelin wrote:
> Hi,
>
> On Mon, 21 Mar 2011, Divakar Ramachandran wrote:
>
>> On Monday 21 March 2011 04:10 PM, Daniel James White wrote:
>>> On Mar 21, 2011, at 5:00 AM, IMAGEJ automatic digest system wrote:
>>>
>>>> From: Divakar Ramachandran <
[hidden email]>
>>>>
>>>> I have just started using ImageJ under Linux (Ubuntu 10.04 LTS
>>>> 64-bit) and would like to get clarification regarding to the
>>>> following points:
>>>>
>>>> 1. Is there a Ubuntu (deb) package for default plugins and macros?
>>>> Both paths listed in man page (under /usr/share/... and ~/.imageJ
>>>> are practically empty.
>>>> 2. I have copied some of my essential plugins directly from ImageJ
>>>> website into the latter path and this seems to work fine. Will
>>>> there be any stability or other issues with this? Should I be
>>>> doing 'sudo cp' into /usr/share instead? I guess these will not be
>>>> updated when I auto-update ImageJ - which could be a blessing for
>>>> plugins such as Microscope_Scale.
>>>> 3. How do I compile a modified plugin from the command line,
>>>> preferably using the system installed jdk?
>>> you need to use Fiji (is just imageJ - batteries included)
>>>
>>> it s a distribution of imageJ that contains the stuff you need , as
>>> you describe below.
>>>
>>> see
>>>
>>>
>>>
http://pacific.mpi-cbg.de Fiji - is just ImageJ (Batteries Included)
>> Thanks, Dan. I have had a quick look at Fiji. It seems to be a good
>> package for life science work.
> Not only life science.
>
>> However, the only pointer to plugin compilation I found was to use the
>> Compile and Run menu option.
> There is also a Fiji Build system which allows defining dependencies
> between multiple components.
>
>> This works only when you install ImageJ along with a JRE.
> You meant a JDK.
Yes. Sorry for the typo.
> Fiji comes with a JRE, but includes javac specifically. So if you have a
> plugin that consists of a single class (possibly including nested
> classes), you can load it into the Script Editor and run it. Or you copy
> the .java file into plugins/ and run it transparently, as if it was a
> script.
>
>> A couple of years ago there was a posting on this mail list giving a
>> command-line syntax for compiling ImageJ on a windows OS computer.
> It is easy:
>
> javac -cp /path/to/ij.jar path/to/source.java
>
This works great, Thanks! It took me some time to locate - the path to
ij.jar on Ubuntu 10.04 LTS 64-bit is /usr/share/java/ij.jar.
> The more relevant question, though, is probably: what exactly do you want
> to do? Yes, you said you want to compile via command-line. There is a good
> possibility, though, that there is a better solution for your problem, if
> only that problem is clearly stated.
>
> Hth,
> Johannes
Thanks Johannes. The immediate problem I had was to be able to compile a
given java source in plugins directory to a class file that can be run
form the plugins menu. For example, the command-line compilation works
quick and simple for things like re-compiling Microscope_Scale.java with
the regularly updated calibration numbers for our TEM.
My background is in Metallurgy and high-resolution TEM. Goal for me with
ImageJ is to be able to translate my Semper scripts into working ImageJ
macros / plugins since we no longer have computers that can run Semper
for Windows. Some stuff are amenable for ad-hoc macros or combinations
of operations from existing ImageJ functionality and plugins available.
Others would require custom plugins. At the moment we are using ImageJ
for scale markers and measurements on diffraction patterns and lattice
images. More complex quantification methods I will be trying to
implement will be filtering based on user selected regions of power
spectra of lattice images and quantification of strain. I am sure to
come up with more specific problems and successes as I work, which I can
share on the list.
Regards,
Divakar