Run without GUI

[ViriatoII]

Hello,

Is it possible to run this directly in python? In headless mode or perhaps being called as a macro like here:

https://forum.image.sc/t/accessing-adding-to-roi-manager-with-pyimagej-script/41505

Cheers,
Ricardo

[ViriatoII]

Ok, got it. It's quite simple:

import imagej, scyjava

scyjava.config.add_option('-Xmx6g')

ij = imagej.init(mode='interactive')
imp = ij.IJ.openImage('INPUT_IMAGE.tiff')  

imp2 = imp.duplicate()
ip = imp2.getProcessor()
width = imp2.getWidth()
height = imp2.getHeight() - 1

RM = ij.RoiManager()        # we create an instance of the RoiManager class
rm = RM.getRoiManager()     # "activate" the RoiManager otherwise it can behave strangely

max_label = int(imp2.getStatistics().max)
max_digits = int(math.ceil(math.log(max_label,10))) # Calculate the number of digits for the name of the ROI (padding with zeros)
ij.IJ.setForegroundColor(0, 0, 0) # We pick black color to delete the label already computed

roiID = -1 

# Iterate over picture and identify pixel values
for j in range(height):
    for i in range(width):
        current_pixel_value = ip.getValue(i,j)
        if current_pixel_value > 0:
            roiID +=1 
            
            # Select all pixels with same value in image
            ij.IJ.doWand(imp2, i, j, 0.0, "Legacy smooth");

            # Add as ROI to the ROI manager
            roi = imp2.getRoi()
            
            # Set roiname to roiID_X_Y (center_point). 
            roi.setName(str(roiID) + "_" +                          #str(int(current_pixel_value)).zfill(max_digits)) # Old
                        str(round(roi.getXBase() + roi.getFloatWidth()/2)) + "_" +
                        str(round(roi.getYBase() + roi.getFloatHeight()/2)))
            rm.addRoi(roi)        #Error.. Static method was being called without being instantiated
    
            # Fill inner part of roi with 0s so it becomes an outline
            ip.setColor(0); # Fix 32 bit issue
            ip.fill(roi) # Much faster than IJ.run(imp2, "Fill", ....       
                 
rm.save("outputDIR/tmp.zip")