Albert | 1 Jan 17:18 2005

ImageJ compiling plugins in FreeBSD

Dear Listers

Running ImageJ with jdk1.4.2 under FreeBSD 5.3.

I can't do "Compile and Run" - complains about java distribution not
having a compiler, which is not true. Any suggestions on what is

Thank you.

Albert Cardona

Albert | 1 Jan 17:32 2005

Re: ImageJ compiling plugins in FreeBSD

Sorry, I forgot to include the tools.jar in the classpath ... fixed.

For the record, the jdk1.4.2 in freebsd is at least as fast as the
1.3.1 in windows (the fastest windows java distribution so far tested
in this computer). Runs the benchmark in ~ 2.2 seconds on the
madril/baboon.jpg. Very promising.

Albert Cardona.

Wayne M Barnes | 1 Jan 21:22 2005

Re: How to .setPixel(int,int) ?

Dear Duane,

    I changed your "standalone" code to have Duane and duane instead of Process and
process.  (Just trying to reduce my confusion a little.)

    It compiles and produces Duane.class.

    But when I try to run it with
java -cp ij.jar Duane

I get only the error:

Exception in thread "main" java.lang.NoClassDefFoundError: Duane

    So how am I supposed to run this?

    In case you can see a typo, I reposted it at

    Thank you,
Wayne M Barnes
wayne <at>    fax: (314) 754-9556

Robert Dougherty | 1 Jan 21:23 2005

Re: servlet sanity check


Thanks.  There is a lot to learn.

I'll probably just save the images on a hard disk.  They are not very large:
100 x 100, maybe.


> -----Original Message-----
> From: ImageJ Interest Group [mailto:IMAGEJ <at> LIST.NIH.GOV] On Behalf Of
> Prodanov, D. (FYS)
> Sent: Friday, December 31, 2004 7:41 AM
> Subject: Re: servlet sanity check
> Hi Robert,
> I guess you don't need full straming media capabilities. If this is so,
> then what you have to do is only refreshing the web-page once per second.
> It is better manageble in JSP than in servlets.
> JSP is a mix between java and HTML and it is compiled to java class
> automatically by Tomcat.
> How are you going to store the acquired images?
> DP

(Continue reading)

Marcel Lee | 2 Jan 13:49 2005

Pixel colour count

Hello ImageJ list.
I'm new to this list so please bare with me.
My problem is the following: I have some color doppler images that I would
like to analyze. I'm interested in pixel sizes of certain regions of
interest (ROI). I've used the histogram function under analyze to obtain a
pixel count of the ROI and this seems to work really well. What I need is
an additional function that counts the colour pixels in this specific ROI
so I can get a ratio of colour pixels in the specific ROI. Is this a
possibility with ImageJ?
I've tried the plugin "color counter" but this does not count pixels but
color variations.
Does anybody have any suggestions as to how I can slove the problem? Are
there any other programs that can tackle my problem?

Thanks for your time and help

Yours sincerely
Marcel Lee

Cheok Yan Cheng | 2 Jan 19:55 2005

Setting tools.jar Classpath In Ant

In order able to execute the Plugins->Compile and Run...

I set my classpath to point to the jar file tools.jar.

My ImageJ run no problem while executing from the binary.

However, when i am trying to execute through source by using ANT, ImageJ
complains it cannot find the javac compiler.

Here is some of the output:
[yccheok <at> localhost source]$ echo $CLASSPATH
[yccheok <at> localhost source]$ ant
Buildfile: build.xml



I try to modify the ant build.xml file to include the tools class path
during java execution

  <target name="run" depends="build" description="Build and run ImageJ.">
    <!--<java jar="ij.jar" fork="yes" />-->
    <java jar="ij.jar" fork="yes"
classpath="/usr/java/j2sdk1.4.2_06/lib/tools.jar" />
(Continue reading)

Cheok Yan Cheng | 2 Jan 20:10 2005

Lock/ Unlock Issues While Running Another Plugin

When I trying to run another plugin in my own written plugin, i realize the
image is being locked and I am prevented from ruing "another plugin"

I try to use the following workaround, but I am not sure whether this is a
correct method to do so? Please advice. Thank you very much!

public class Motion implements PlugInFilter {
    private ImagePlus imp;

    public int setup(String arg, ImagePlus imp) {
        this.imp = imp;
        return DOES_8G;

    public void run(ImageProcessor ip) {
        // While Motion plugin in is running, the active image is being locked.
        // Hence, we need to unlock it explicitly in order to use another plugin
        // to process it.
        IJ.runPlugIn("ij.plugin.Thresholder", "");

        // Re-lock it again after we have finished process the active image
        // using other plugin.

Wayne M Barnes | 3 Jan 00:21 2005

THE ANSWER to: How to .setPixel(int,int)

Dear Duane, Wayne R., Mike and Jason,

    I got it.  Here is the answer to my problem, how
to make work faster than "Fill" "Slice".
It uses some respelled and relocated advice frome Wayne R.

1.  Put the line
ImageProcessor ip;
// at the beginning of the plugin, before
//any methods (like right after "ImagePlus img2;", to make it global.

2.  In the 'run' section, remove "ImageProcessor" from the line
ImageProcessor ip = imp1.getProcessor;
// so 'ip' is the global one.

3.  To put a pixel during some method, use a line like:
ip.putPixel(ix,iy,red<<16 | green <<8 | blue);
// This works very fast, even in a loop that does 10,000 pixels.

4.  To see the new pixel(s)

    I'll submit the complete faster version soon.

               - Wayne M. Barnes

>    At "the beginning of the plugin" I already have a line in my 'run'
> section:
> ImageProcessor ip = imp1.getProcessor();
(Continue reading)

mark alvin ligaya | 3 Jan 04:48 2005

RGB to Grayscale

 Hello everyone,

       Does anybody know how to convert an RGB image into a grayscale image?


Orkun Ersoy | 3 Jan 08:52 2005

Re: RGB to Grayscale

Open image then;

Image/type/ 8 bit , 16 bit or 32 bit

Hacettepe University
Department of Geological Engineering
Beytepe-Ankara / TURKEY
Ph: +90 312 2977700 / 126

-----Original Message-----
From: ImageJ Interest Group [mailto:IMAGEJ <at> LIST.NIH.GOV] On Behalf Of
mark alvin ligaya
Sent: Monday, January 03, 2005 5:48 AM
Subject: RGB to Grayscale

 Hello everyone,

       Does anybody know how to convert an RGB image into a grayscale