Using imageJ from the command line in Ubuntu

[bateman]

Hello,

I haven't really used ImageJ from the command prompt before, if I want to pass 4 String variables in my Gamma4 class run method is it a simple case of putting:

public void run(String[] args)
{
        double X1,X2,Y1,Y2;
        if (args.length>0)
        try{
                X1 = Double.parseDouble(args[0]);
                X2 = Double.parseDouble(args[1]);
                Y1 = Double.parseDouble(args[2]);
                Y2 = Double.parseDouble(args[3]);
        }
       
Only every time I try to "Compile & Run" my program I have the following error message,

/home/gary/.imagej/plugins/Gamma4.java:13: error: Gamma4 is not abstract and does not override abstract method run(String) in PlugIn
public class Gamma4 implements PlugIn {
       ^
1 error
1 warning

Any ideas what I have done wrong?

Thank you in advance

[Volker Baecker]

Hello,
the error is there because you do not implement the method run of the
interface PlugIn. Your method run has a different signature. It has
String[] as argument instead of the String in PlugIn. You should write
your plugin normally and use a GenericDialog for the parameters. You can
then call it from the commandline with something like this:
      ImageJ -eval "run('Plug In', 'arguments');" -batch

Volker
On 05/17/2013 01:24 PM, bateman wrote:

> Hello,
>
> I haven't really used ImageJ from the command prompt before, if I want to
> pass 4 String variables in my Gamma4 class run method is it a simple case of
> putting:
>
> public void run(String[] args)
> {
> double X1,X2,Y1,Y2;
> if (args.length>0)
> try{
> X1 = Double.parseDouble(args[0]);
> X2 = Double.parseDouble(args[1]);
> Y1 = Double.parseDouble(args[2]);
> Y2 = Double.parseDouble(args[3]);
> }
>
> Only every time I try to "Compile & Run" my program I have the following
> error message,
>
> /home/gary/.imagej/plugins/Gamma4.java:13: error: Gamma4 is not abstract and
> does not override abstract method run(String) in PlugIn
> public class Gamma4 implements PlugIn {
>        ^
> 1 error
> 1 warning
>
> Any ideas what I have done wrong?
>
> Thank you in advance
>
>
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Using-imageJ-from-the-command-line-in-Ubuntu-tp5003041.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[bateman]

So I cannot specify more than one string object in my "run" command? Is that the case?

[justin.senseney]

>So I cannot specify more than one string object in my "run" command? Is that
>the case?

Yes, but you can still parse the one string object yourself, using something like String[] args = originalArgString.split(" "), then the rest of your code can be left as is.

-Justin



--
View this message in context: http://imagej.1557.x6.nabble.com/Using-imageJ-from-the-command-line-in-Ubuntu-tp5003041p5003043.html
Sent from the ImageJ mailing list archive at Nabble.com.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Adrian Daerr-2]

On 17.05.2013 14:52, bateman wrote:
> So I cannot specify more than one string object in my "run" command? Is that
> the case?

Right, but that does not mean that you cannot pass more than one
parameter: it just means you have to specify the parameters in a way
that GenericDialog will understand, that is using the field labels as
variable names. Here is an example from a recent post (
http://permalink.gmane.org/gmane.comp.java.imagej/28605 ):

| int sizeE = 2;
| IJ.run(imp2, "Gray Morphology",
|        "radius="+sizeE+" type=circle operator=erode");

(this is from within Java code, strip "IJ." etc for the command line /
macro version)

(and in case you want to pass strings, you have to bracket them using [])

HTH
Adrian

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html