from ij import IJ;
from ij.plugin.frame import RoiManager;
from java.awt import Color
from ij.gui import PolygonRoi, WaitForUserDialog;
from ij.gui import Roi;
from java.awt import FileDialog
import os
EXCLUDE_ON_EDGES = True
NUCLEI_GROUP = 2
CYTOPLASM_GROUP = 1
COLORS = [Color.cyan, Color.magenta]
DISTANCE_TO_BORDER = 5
Roi.setGroupName(NUCLEI_GROUP, "nuclei")
Roi.setGroupName(CYTOPLASM_GROUP, "cytoplasm")
Roi.saveGroupNames()
folder = IJ.getDirectory("")
files=[[], [], [], []]
for c in range(0, 4):
files[c] = [os.path.join(folder, image) for image in os.listdir(folder) if image.lower().endswith("_c"+str(c)+"_cp_outlines.txt")]
if(not files[0] and not files[1] and not files[2] and not files[3]):
files[0] = [os.path.join(folder, image) for image in os.listdir(folder) if image.lower().endswith("_cp_outlines.txt")]
images = [os.path.join(folder, image) for image in os.listdir(folder)
if (image.lower().endswith(".tif")
or image.lower().endswith(".jpg")
or image.lower().endswith(".png"))
and not image.lower().endswith("_cp_masks.png")]
ext = images[0].split(".")[1]
RM = RoiManager()
