Dear all,
is there a way to use this plugin:
from morpholibj suite without showing the image and getting it in a variable?
it would be super useful inside a script, instead of getting it using WindowManager and then hide it.
thank you,
Emanuele
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Hi,
are you using a scripting language? Then it is easy, you need essentially this line (line49) + the packge imports:
resultPlus = LabelImages.keepLargestLabel(imagePlus);
The API of morpholibj lives here (direct link to LabelImages: https://javadoc.scijava.org/MorphoLibJ/inra/ijpb/label/LabelImages.html )
For macro I don’t know.
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Hey @emartini,
that’s a cool plugin in #morpholibj indeed. If you can’t call it in macro directly, you may want to explore calling it via CLIJ:
// Init GPU
run("CLIJ2 Macro Extensions", "cl_device=");
// Load image from disc
open("C:/structure/data/blobs.tif");
image1 = getTitle();
Ext.CLIJ2_push(image1);
// Threshold Otsu
Ext.CLIJ2_thresholdOtsu(image1, image2);
Ext.CLIJ2_release(image1);
Ext.CLIJ2_pull(image2);
// Connected Components Labeling Box
Ext.CLIJ2_connectedComponentsLabelingBox(image2, image3);
Ext.CLIJ2_release(image2);
Ext.CLIJ2_pull(image3);
run("glasbey_on_dark");
// Keep Largest Region
Ext.CLIJx_morphoLibJKeepLargestRegion(image3, image4);
Ext.CLIJ2_release(image3);
Ext.CLIJ2_pull(image4);
Ext.CLIJ2_release(image4);
You can get the result in a variable (image4) by not calling the “pull” command.
In order to make it run, you need to install clij, clij2 and the clijx-assistant-extesions as described here:
Let me know if it’s useful! This is experimental code and I need user feedback to see if this should survive or not 
Cheers,
Robert
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Hi @noreenw,
yes I am using jython scripting language.
I had found that api page but there is still a step that I think I am missing, what is the input of that call?
resultPlus = LabelImages.keepLargestLabel(imagePlus)
how it is supposed to be the ImagePlus that I pass?
for example this snippet, doesn’t produce an image with only the largest region, but it doesn’t throw any error: it simply returns the input ImagePlus
from ij import IJ
from inra.ijpb.label import LabelImages
imp = IJ.createImage("Untitled", "8-bit black", 512, 512, 1);
imp.setRoi(65,26,198,212);
IJ.run(imp, "Set...", "value=255");
imp.setRoi(366,353,39,45);
IJ.run(imp, "Set...", "value=255");
largest_region = LabelImages.keepLargestLabel(imp)
largest_region.show()
Do I have to “labelise” someway the imageplus?
thank you for your help
Emanuele
dear @haesleinhuepf,
at the moment I am trying it in jython and with no-gpu approach.
But of course if I’ll have time I will give it a try with clij2
ciao,
Emanuele Martini
1 Like
dear @noreenw
found a solution: if you are working with binary images, you can use directly this *BinaryImages api:
with the keepLargestRegion(ij.ImagePlus imagePlus) method
this way:
from ij import IJ
from inra.ijpb.binary import BinaryImages
imp = IJ.createImage("Untitled", "8-bit black", 512, 512, 1);
imp.setRoi(65,26,198,212);
IJ.run(imp, "Set...", "value=255");
imp.setRoi(366,353,39,45);
IJ.run(imp, "Set...", "value=255");
imp.show();
largest_region = BinaryImages.keepLargestRegion(imp)
largest_region.show()
hth,
Emanuele Martini
3 Likes
Happy to hear that you found the solution already!
Yes indeed, for black-white images the BinaryImages class would be the way to go (or alternatively do a connected component labeling and then use LabelImages).
3 Likes
Indeed.
What you show is a binary image. Both of the rectangles have the “label” 255, so they’re in fact treated as the same (but disconnected) object by any algorithm that expects a “label image” (or “label map”).
You first need to create an image where each object has a distinct label, e.g. by doing a connected component analysis. In Analyze Particles, use the Count Mask option to get this. CLIJ has a function for that as well, of course.
2 Likes