Calling "Label image to ROIs" from jython

[giocard]

The only way I could find to call the command from jython is to use the following line IJ.run(imp, "Label image to ROIs", "") but imp is ignored. Instead, the command is always applied to the active image.

[romainGuiet]

Hi @giocard ,

I'm not familiar with jython, but I tested the "groovy" script below with the latest version 0.2.4 (available on our update site).

import ij.*
import ch.epfl.biop.ij2command.*

#@CommandService command
#@RoiManager rm

rm.reset();
IJ.run("Close All", "");

// Open blobs and detect ROIs
imp = IJ.openImage("http://imagej.nih.gov/ij/images/blobs.gif");
imp.show()
IJ.setAutoThreshold(imp, "Default");
IJ.run(imp, "Analyze Particles...", "add");

// from ROIs make a Label image
label_imp = command.run( Rois2Labels , false , 'imp' , imp , 'rm', rm).get().getOutput("label_imp")
label_imp.show()

// reset the ROImanager
rm.reset();

// from the label image make ROIs
command.run( Labels2Rois , false , 'imp' , label_imp , 'rm', rm).get()

Please let me know if it works better for you this way,

Cheers,

Romain

[giocard]

Hi @romainGuiet,

the command service works nicely also in jython. The only minor issue is then that, being ij2, the command is not macro-recordable.

Thank you very much! Giovanni

[romainGuiet]

Hi @giocard

the command service works nicely also in jython.

Great!

The only minor issue is then that, being ij2, the command is not macro-recordable.

Indeed the commands are murch easier to create but have this macro-recording issue (@NicoKiaru and I really hope it will be fixed soon)

I created a script folder with an ijm and groovy example, and I will modify the readme to point to them.

Cheers,

Romain