--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/overlay_segmentation_mask.py	Sat Feb 09 14:41:11 2019 -0500
@@ -0,0 +1,41 @@
+import argparse
+import sys
+import os
+
+import matplotlib
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
+
+#TODO make importable by python script
+
+import skimage.io
+import skimage.measure
+
+parser = argparse.ArgumentParser()
+parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
+parser.add_argument('mask_file', type=argparse.FileType('r'), help='mask file')
+parser.add_argument('out_file', type=str, help='out file (PNG)') # file would be created immediately with argparse.FileType('w') s.t. file cannot be renamed on galaxy
+parser.add_argument('--grey', dest='greyscale', action='store_true', help='image is greyscale')
+parser.add_argument('--label', dest='label', action='store_true', help='plot label')
+parser.add_argument('--label_color', dest='label_color', default='#FFFF00', help='label color')
+parser.add_argument('--thickness', dest='thickness', default=0.3, type=float, help='thickness')
+parser.add_argument('--stroke_color', dest='stroke_color', default='#ff0000', help='stroke color')
+args = parser.parse_args()
+img = skimage.io.imread(args.input_file.name)
+label = skimage.io.imread(args.mask_file.name)
+
+fig = plt.figure()
+ax = fig.add_axes([0, 0, 1, 1])
+ax.axis('off')
+
+if args.label:
+    for reg in skimage.measure.regionprops(label):
+        ax.text(reg.centroid[1], reg.centroid[0], str(reg.label), color=args.label_color)
+
+if args.greyscale:
+    plt.imshow(img, cmap=plt.cm.gray)
+else:
+    plt.imshow(img)
+plt.contour(label, linewidths=args.thickness, colors=args.stroke_color)
+
+fig.canvas.print_png(args.out_file)
\ No newline at end of file