imagej_roi_converter.py

gistfile1.txt

from ij import IJ
from ij.plugin.frame import RoiManager
from ij.gui import PolygonRoi
from ij.gui import Roi
from java.awt import FileDialog

fd = FileDialog(IJ.getInstance(), "Open", FileDialog.LOAD)
fd.show()
file_name = fd.getDirectory() + fd.getFile()
print(file_name)

RM = RoiManager()
rm = RM.getRoiManager()

imp = IJ.getImage()

textfile = open(file_name, "r")
for line in textfile:
    xy = map(int, line.rstrip().split(","))
    X = xy[::2]
    Y = xy[1::2]
    imp.setRoi(PolygonRoi(X, Y, Roi.POLYGON))
    # IJ.run(imp, "Convex Hull", "")
    roi = imp.getRoi()
    #######
    roi_rect = roi.getBounds()
    if roi_rect.x > 0 and roi_rect.y > 0 and roi_rect.x + roi_rect.width < imp.width - 1 and roi_rect.y + roi_rect.height < imp.height - 1:
       rm.addRoi(roi)
    else:
       print("roi touching edge, not adding to manager")
    #####
    print(roi)
   
textfile.close()
rm.runCommand("Associate", "true")
rm.runCommand("Show All with labels")