--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coordinates_of_roi.py	Sat Feb 09 14:33:43 2019 -0500
@@ -0,0 +1,40 @@
+import argparse
+import pandas as pd
+import skimage.io
+import skimage.color
+import warnings
+
+def get_pixel_values(im, pixel_table, white_obj, threshold, offset=[0,0]):
+    data = skimage.io.imread(im)
+    if len(data.shape) == 3 and data.shape[-1] > 1:
+        data = skimage.color.rgb2grey(data)
+    x = []
+    y = []
+    for i in range(data.shape[0]):
+        for j in range(data.shape[1]):
+            if white_obj == False:
+                if data[i,j] <= threshold:
+                    x.append(j + offset[0])
+                    y.append(i + offset[1])
+            elif data[i,j] >= threshold:
+                    x.append(j + offset[0])
+                    y.append(i + offset[1])
+                    
+    df = pd.DataFrame()
+    df['x'] = x
+    df['y'] = y
+    df.to_csv(pixel_table, sep="\t", index = False)
+                     
+if __name__=="__main__":
+    parser = argparse.ArgumentParser(description = "Create a csv table with Coordinates of the ROI")
+    parser.add_argument("im", help = "Paste path to out.png (output created by transformation)")
+    parser.add_argument("pixel_table", help = "Paste path to file in which list with all pixles > threshold should be saved")
+    parser.add_argument('offset_x', type=int, help='offset in x direction (width)', default=0)
+    parser.add_argument('offset_y', type=int, help='offset in y direction (height)', default=0)
+    parser.add_argument("--white_obj", dest = "white_obj", default=False, help = "If set objects in image are white otherwise black", action = "store_true")
+    parser.add_argument("--threshold", dest = "threshold", default = 0.5, help = "Enter desired threshold value", type = float)
+    
+    args = parser.parse_args()  
+    # with warnings.catch_warnings():
+	#     warnings.simplefilter("ignore") 
+    get_pixel_values(args.im, args.pixel_table, args.white_obj, args.threshold, [args.offset_x, args.offset_y])