Empty line in roi txt file causing bug in imagej_roi_converter.py[BUG] #708
Description
Describe the bug
The .txt file with the ROIs generates some empty lines that cause an error in line 19 of the imagej_roi_converter.py (xy = map(int, line.rstrip().split(",")))
To Reproduce
I modified slightly the imagej_roi_converter.py to be able to input files programmatically. When it tries to input some .txt files with the rois containing an empty line the map function fails and only the rois before that empty line are reported. It has an easy fix which is to ignore those lines:
if len(line.strip()) == 0:
continue
If anybody needs to load the rois programmatically, this is the full implementation:
#@String my_file
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
print(my_file)
RM = RoiManager()
rm = RM.getRoiManager()
imp = IJ.getImage()
textfile = open(my_file, "r")
for line in textfile:
if len(line.strip()) == 0:
continue
print(line)
xy = list(map(int, line.rstrip().split(",")))
print(xy)
X = xy[::2]
Y = xy[1::2]
imp.setRoi(PolygonRoi(X, Y, Roi.POLYGON))
# IJ.run(imp, "Convex Hull", "")
roi = imp.getRoi()
print(roi)
rm.addRoi(roi)
textfile.close()
rm.runCommand("Associate", "true")
rm.runCommand("Show All with labels")