orobix · ashishbhaskar11 · Aug 30, 2022 · Aug 30, 2022 · Sep 8, 2022
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,4 @@
 *~
 *.pyc
 .DS_Store
-DRIVE_datasets_training_testing
+DRIVE_datasets_training_testing
diff --git a/DRIVE/test/1st_manual/01_manual1.gif b/DRIVE/test/1st_manual/01_manual1.gif
diff --git a/DRIVE/test/1st_manual/02_manual1.gif b/DRIVE/test/1st_manual/02_manual1.gif
diff --git a/DRIVE/test/1st_manual/03_manual1.gif b/DRIVE/test/1st_manual/03_manual1.gif
diff --git a/DRIVE/test/1st_manual/04_manual1.gif b/DRIVE/test/1st_manual/04_manual1.gif
diff --git a/DRIVE/test/1st_manual/05_manual1.gif b/DRIVE/test/1st_manual/05_manual1.gif
diff --git a/DRIVE/test/1st_manual/06_manual1.gif b/DRIVE/test/1st_manual/06_manual1.gif
diff --git a/DRIVE/test/1st_manual/07_manual1.gif b/DRIVE/test/1st_manual/07_manual1.gif
diff --git a/DRIVE/test/1st_manual/08_manual1.gif b/DRIVE/test/1st_manual/08_manual1.gif
diff --git a/DRIVE/test/1st_manual/09_manual1.gif b/DRIVE/test/1st_manual/09_manual1.gif
diff --git a/DRIVE/test/1st_manual/10_manual1.gif b/DRIVE/test/1st_manual/10_manual1.gif
diff --git a/DRIVE/test/1st_manual/11_manual1.gif b/DRIVE/test/1st_manual/11_manual1.gif
diff --git a/DRIVE/test/1st_manual/12_manual1.gif b/DRIVE/test/1st_manual/12_manual1.gif
diff --git a/DRIVE/test/1st_manual/13_manual1.gif b/DRIVE/test/1st_manual/13_manual1.gif
diff --git a/DRIVE/test/1st_manual/14_manual1.gif b/DRIVE/test/1st_manual/14_manual1.gif
diff --git a/DRIVE/test/1st_manual/15_manual1.gif b/DRIVE/test/1st_manual/15_manual1.gif
diff --git a/DRIVE/test/1st_manual/16_manual1.gif b/DRIVE/test/1st_manual/16_manual1.gif
diff --git a/DRIVE/test/1st_manual/17_manual1.gif b/DRIVE/test/1st_manual/17_manual1.gif
diff --git a/DRIVE/test/1st_manual/18_manual1.gif b/DRIVE/test/1st_manual/18_manual1.gif
diff --git a/DRIVE/test/1st_manual/19_manual1.gif b/DRIVE/test/1st_manual/19_manual1.gif
diff --git a/DRIVE/test/1st_manual/20_manual1.gif b/DRIVE/test/1st_manual/20_manual1.gif
diff --git a/DRIVE/test/1st_manual/jpg format/vessel(1).jpg b/DRIVE/test/1st_manual/jpg format/vessel(1).jpg
diff --git a/DRIVE/test/1st_manual/jpg format/vessel(10).jpg b/DRIVE/test/1st_manual/jpg format/vessel(10).jpg
diff --git a/DRIVE/test/1st_manual/jpg format/vessel(2).jpg b/DRIVE/test/1st_manual/jpg format/vessel(2).jpg
diff --git a/DRIVE/test/1st_manual/jpg format/vessel(3).jpg b/DRIVE/test/1st_manual/jpg format/vessel(3).jpg
diff --git a/DRIVE/test/1st_manual/jpg format/vessel(4).jpg b/DRIVE/test/1st_manual/jpg format/vessel(4).jpg
diff --git a/DRIVE/test/1st_manual/jpg format/vessel(5).jpg b/DRIVE/test/1st_manual/jpg format/vessel(5).jpg
diff --git a/DRIVE/test/1st_manual/jpg format/vessel(6).jpg b/DRIVE/test/1st_manual/jpg format/vessel(6).jpg
diff --git a/DRIVE/test/1st_manual/jpg format/vessel(7).jpg b/DRIVE/test/1st_manual/jpg format/vessel(7).jpg
diff --git a/DRIVE/test/1st_manual/jpg format/vessel(8).jpg b/DRIVE/test/1st_manual/jpg format/vessel(8).jpg
diff --git a/DRIVE/test/1st_manual/jpg format/vessel(9).jpg b/DRIVE/test/1st_manual/jpg format/vessel(9).jpg
diff --git a/DRIVE/test/2nd_manual/05_manual2.gif b/DRIVE/test/2nd_manual/05_manual2.gif
diff --git a/DRIVE/test/2nd_manual/06_manual2.gif b/DRIVE/test/2nd_manual/06_manual2.gif
diff --git a/DRIVE/test/2nd_manual/07_manual2.gif b/DRIVE/test/2nd_manual/07_manual2.gif
diff --git a/DRIVE/test/2nd_manual/08_manual2.gif b/DRIVE/test/2nd_manual/08_manual2.gif
diff --git a/DRIVE/test/2nd_manual/09_manual2.gif b/DRIVE/test/2nd_manual/09_manual2.gif
diff --git a/DRIVE/test/2nd_manual/10_manual2.gif b/DRIVE/test/2nd_manual/10_manual2.gif
diff --git a/DRIVE/test/2nd_manual/11_manual2.gif b/DRIVE/test/2nd_manual/11_manual2.gif
diff --git a/DRIVE/test/2nd_manual/12_manual2.gif b/DRIVE/test/2nd_manual/12_manual2.gif
diff --git a/DRIVE/test/2nd_manual/13_manual2.gif b/DRIVE/test/2nd_manual/13_manual2.gif
diff --git a/DRIVE/test/2nd_manual/15_manual2.gif b/DRIVE/test/2nd_manual/15_manual2.gif
diff --git a/DRIVE/test/2nd_manual/16_manual2.gif b/DRIVE/test/2nd_manual/16_manual2.gif
diff --git a/DRIVE/test/2nd_manual/17_manual2.gif b/DRIVE/test/2nd_manual/17_manual2.gif
diff --git a/DRIVE/test/2nd_manual/18_manual2.gif b/DRIVE/test/2nd_manual/18_manual2.gif
diff --git a/DRIVE/test/2nd_manual/19_manual2.gif b/DRIVE/test/2nd_manual/19_manual2.gif
diff --git a/DRIVE/test/2nd_manual/20_manual2.gif b/DRIVE/test/2nd_manual/20_manual2.gif
diff --git a/DRIVE/test/2nd_manual/vessel(1).gif b/DRIVE/test/2nd_manual/vessel(1).gif
diff --git a/DRIVE/test/2nd_manual/vessel(14).gif b/DRIVE/test/2nd_manual/vessel(14).gif
diff --git a/DRIVE/test/2nd_manual/vessel(2).gif b/DRIVE/test/2nd_manual/vessel(2).gif
diff --git a/DRIVE/test/2nd_manual/vessel(3).gif b/DRIVE/test/2nd_manual/vessel(3).gif
diff --git a/DRIVE/test/2nd_manual/vessel(4).gif b/DRIVE/test/2nd_manual/vessel(4).gif
diff --git a/DRIVE/test/images/01_test.tif b/DRIVE/test/images/01_test.tif
diff --git a/DRIVE/test/images/02_test.tif b/DRIVE/test/images/02_test.tif
diff --git a/DRIVE/test/images/03_test.tif b/DRIVE/test/images/03_test.tif
diff --git a/DRIVE/test/images/04_test.tif b/DRIVE/test/images/04_test.tif
diff --git a/DRIVE/test/images/05_test.tif b/DRIVE/test/images/05_test.tif
diff --git a/DRIVE/test/images/06_test.tif b/DRIVE/test/images/06_test.tif
diff --git a/DRIVE/test/images/07_test.tif b/DRIVE/test/images/07_test.tif
diff --git a/DRIVE/test/images/08_test.tif b/DRIVE/test/images/08_test.tif
diff --git a/DRIVE/test/images/09_test.tif b/DRIVE/test/images/09_test.tif
diff --git a/DRIVE/test/images/10_test.tif b/DRIVE/test/images/10_test.tif
diff --git a/DRIVE/test/images/11_test.tif b/DRIVE/test/images/11_test.tif
diff --git a/DRIVE/test/images/12_test.tif b/DRIVE/test/images/12_test.tif
diff --git a/DRIVE/test/images/13_test.tif b/DRIVE/test/images/13_test.tif
diff --git a/DRIVE/test/images/14_test.tif b/DRIVE/test/images/14_test.tif
diff --git a/DRIVE/test/images/15_test.tif b/DRIVE/test/images/15_test.tif
diff --git a/DRIVE/test/images/16_test.tif b/DRIVE/test/images/16_test.tif
diff --git a/DRIVE/test/images/17_test.tif b/DRIVE/test/images/17_test.tif
diff --git a/DRIVE/test/images/18_test.tif b/DRIVE/test/images/18_test.tif
diff --git a/DRIVE/test/images/19_test.tif b/DRIVE/test/images/19_test.tif
diff --git a/DRIVE/test/images/20_test.tif b/DRIVE/test/images/20_test.tif
diff --git a/DRIVE/test/mask/01_test_mask.gif b/DRIVE/test/mask/01_test_mask.gif
diff --git a/DRIVE/test/mask/02_test_mask.gif b/DRIVE/test/mask/02_test_mask.gif
diff --git a/DRIVE/test/mask/03_test_mask.gif b/DRIVE/test/mask/03_test_mask.gif
diff --git a/DRIVE/test/mask/04_test_mask.gif b/DRIVE/test/mask/04_test_mask.gif
diff --git a/DRIVE/test/mask/05_test_mask.gif b/DRIVE/test/mask/05_test_mask.gif
diff --git a/DRIVE/test/mask/06_test_mask.gif b/DRIVE/test/mask/06_test_mask.gif
diff --git a/DRIVE/test/mask/07_test_mask.gif b/DRIVE/test/mask/07_test_mask.gif
diff --git a/DRIVE/test/mask/08_test_mask.gif b/DRIVE/test/mask/08_test_mask.gif
diff --git a/DRIVE/test/mask/09_test_mask.gif b/DRIVE/test/mask/09_test_mask.gif
diff --git a/DRIVE/test/mask/10_test_mask.gif b/DRIVE/test/mask/10_test_mask.gif
diff --git a/DRIVE/test/mask/11_test_mask.gif b/DRIVE/test/mask/11_test_mask.gif
diff --git a/DRIVE/test/mask/12_test_mask.gif b/DRIVE/test/mask/12_test_mask.gif
diff --git a/DRIVE/test/mask/13_test_mask.gif b/DRIVE/test/mask/13_test_mask.gif
diff --git a/DRIVE/test/mask/14_test_mask.gif b/DRIVE/test/mask/14_test_mask.gif
diff --git a/DRIVE/test/mask/15_test_mask.gif b/DRIVE/test/mask/15_test_mask.gif
diff --git a/DRIVE/test/mask/16_test_mask.gif b/DRIVE/test/mask/16_test_mask.gif
diff --git a/DRIVE/test/mask/17_test_mask.gif b/DRIVE/test/mask/17_test_mask.gif
diff --git a/DRIVE/test/mask/18_test_mask.gif b/DRIVE/test/mask/18_test_mask.gif
diff --git a/DRIVE/test/mask/19_test_mask.gif b/DRIVE/test/mask/19_test_mask.gif
diff --git a/DRIVE/test/mask/20_test_mask.gif b/DRIVE/test/mask/20_test_mask.gif
diff --git a/DRIVE/training/1st_manual/21_manual1.gif b/DRIVE/training/1st_manual/21_manual1.gif
diff --git a/DRIVE/training/1st_manual/22_manual1.gif b/DRIVE/training/1st_manual/22_manual1.gif
diff --git a/DRIVE/training/1st_manual/23_manual1.gif b/DRIVE/training/1st_manual/23_manual1.gif
diff --git a/DRIVE/training/1st_manual/24_manual1.gif b/DRIVE/training/1st_manual/24_manual1.gif
diff --git a/DRIVE/training/1st_manual/25_manual1.gif b/DRIVE/training/1st_manual/25_manual1.gif
diff --git a/DRIVE/training/1st_manual/26_manual1.gif b/DRIVE/training/1st_manual/26_manual1.gif
diff --git a/DRIVE/training/1st_manual/27_manual1.gif b/DRIVE/training/1st_manual/27_manual1.gif
diff --git a/DRIVE/training/1st_manual/28_manual1.gif b/DRIVE/training/1st_manual/28_manual1.gif
diff --git a/DRIVE/training/1st_manual/29_manual1.gif b/DRIVE/training/1st_manual/29_manual1.gif
diff --git a/DRIVE/training/1st_manual/30_manual1.gif b/DRIVE/training/1st_manual/30_manual1.gif
diff --git a/DRIVE/training/1st_manual/31_manual1.gif b/DRIVE/training/1st_manual/31_manual1.gif
diff --git a/DRIVE/training/1st_manual/32_manual1.gif b/DRIVE/training/1st_manual/32_manual1.gif
diff --git a/DRIVE/training/1st_manual/33_manual1.gif b/DRIVE/training/1st_manual/33_manual1.gif
diff --git a/DRIVE/training/1st_manual/34_manual1.gif b/DRIVE/training/1st_manual/34_manual1.gif
diff --git a/DRIVE/training/1st_manual/35_manual1.gif b/DRIVE/training/1st_manual/35_manual1.gif
diff --git a/DRIVE/training/1st_manual/36_manual1.gif b/DRIVE/training/1st_manual/36_manual1.gif
diff --git a/DRIVE/training/1st_manual/37_manual1.gif b/DRIVE/training/1st_manual/37_manual1.gif
diff --git a/DRIVE/training/1st_manual/38_manual1.gif b/DRIVE/training/1st_manual/38_manual1.gif
diff --git a/DRIVE/training/1st_manual/39_manual1.gif b/DRIVE/training/1st_manual/39_manual1.gif
diff --git a/DRIVE/training/1st_manual/40_manual1.gif b/DRIVE/training/1st_manual/40_manual1.gif
diff --git a/DRIVE/training/images/21_training.tif b/DRIVE/training/images/21_training.tif
diff --git a/DRIVE/training/images/22_training.tif b/DRIVE/training/images/22_training.tif
diff --git a/DRIVE/training/images/23_training.tif b/DRIVE/training/images/23_training.tif
diff --git a/DRIVE/training/images/24_training.tif b/DRIVE/training/images/24_training.tif
diff --git a/DRIVE/training/images/25_training.tif b/DRIVE/training/images/25_training.tif
diff --git a/DRIVE/training/images/26_training.tif b/DRIVE/training/images/26_training.tif
diff --git a/DRIVE/training/images/27_training.tif b/DRIVE/training/images/27_training.tif
diff --git a/DRIVE/training/images/28_training.tif b/DRIVE/training/images/28_training.tif
diff --git a/DRIVE/training/images/29_training.tif b/DRIVE/training/images/29_training.tif
diff --git a/DRIVE/training/images/30_training.tif b/DRIVE/training/images/30_training.tif
diff --git a/DRIVE/training/images/31_training.tif b/DRIVE/training/images/31_training.tif
diff --git a/DRIVE/training/images/32_training.tif b/DRIVE/training/images/32_training.tif
diff --git a/DRIVE/training/images/33_training.tif b/DRIVE/training/images/33_training.tif
diff --git a/DRIVE/training/images/34_training.tif b/DRIVE/training/images/34_training.tif
diff --git a/DRIVE/training/images/35_training.tif b/DRIVE/training/images/35_training.tif
diff --git a/DRIVE/training/images/36_training.tif b/DRIVE/training/images/36_training.tif
diff --git a/DRIVE/training/images/37_training.tif b/DRIVE/training/images/37_training.tif
diff --git a/DRIVE/training/images/38_training.tif b/DRIVE/training/images/38_training.tif
diff --git a/DRIVE/training/images/39_training.tif b/DRIVE/training/images/39_training.tif
diff --git a/DRIVE/training/images/40_training.tif b/DRIVE/training/images/40_training.tif
diff --git a/DRIVE/training/mask/21_training_mask.gif b/DRIVE/training/mask/21_training_mask.gif
diff --git a/DRIVE/training/mask/22_training_mask.gif b/DRIVE/training/mask/22_training_mask.gif
diff --git a/DRIVE/training/mask/23_training_mask.gif b/DRIVE/training/mask/23_training_mask.gif
diff --git a/DRIVE/training/mask/24_training_mask.gif b/DRIVE/training/mask/24_training_mask.gif
diff --git a/DRIVE/training/mask/25_training_mask.gif b/DRIVE/training/mask/25_training_mask.gif
diff --git a/DRIVE/training/mask/26_training_mask.gif b/DRIVE/training/mask/26_training_mask.gif
diff --git a/DRIVE/training/mask/27_training_mask.gif b/DRIVE/training/mask/27_training_mask.gif
diff --git a/DRIVE/training/mask/28_training_mask.gif b/DRIVE/training/mask/28_training_mask.gif
diff --git a/DRIVE/training/mask/29_training_mask.gif b/DRIVE/training/mask/29_training_mask.gif
diff --git a/DRIVE/training/mask/30_training_mask.gif b/DRIVE/training/mask/30_training_mask.gif
diff --git a/DRIVE/training/mask/31_training_mask.gif b/DRIVE/training/mask/31_training_mask.gif
diff --git a/DRIVE/training/mask/32_training_mask.gif b/DRIVE/training/mask/32_training_mask.gif
diff --git a/DRIVE/training/mask/33_training_mask.gif b/DRIVE/training/mask/33_training_mask.gif
diff --git a/DRIVE/training/mask/34_training_mask.gif b/DRIVE/training/mask/34_training_mask.gif
diff --git a/DRIVE/training/mask/35_training_mask.gif b/DRIVE/training/mask/35_training_mask.gif
diff --git a/DRIVE/training/mask/36_training_mask.gif b/DRIVE/training/mask/36_training_mask.gif
diff --git a/DRIVE/training/mask/37_training_mask.gif b/DRIVE/training/mask/37_training_mask.gif
diff --git a/DRIVE/training/mask/38_training_mask.gif b/DRIVE/training/mask/38_training_mask.gif
diff --git a/DRIVE/training/mask/39_training_mask.gif b/DRIVE/training/mask/39_training_mask.gif
diff --git a/DRIVE/training/mask/40_training_mask.gif b/DRIVE/training/mask/40_training_mask.gif
diff --git a/Readme.md b/Readme.md
@@ -75,6 +75,14 @@ The following dependencies are needed:
 - ConfigParser >=3.5.0b2
 - scikit-learn >= 0.17.1
 
+Version used
+- python3 = 3.9.13
+- numpy = 1.19.5
+- PIL =8.2.0
+- opencv =4.5.2
+- h5py =3.1.0
+- configparser =3.10.6
+- scikit-learn = 0.24.2
 
 Also, you will need the DRIVE database, which can be freely downloaded as explained in the next section.
 

diff --git a/lib/extract_patches.py b/lib/extract_patches.py
@@ -1,6 +1,6 @@
 import numpy as np
 import random
-import ConfigParser
+#import ConfigParser
 
 from help_functions import load_hdf5
 from help_functions import visualize
@@ -34,18 +34,18 @@ def get_data_training(DRIVE_train_imgs_original,
     #check masks are within 0-1
     assert(np.min(train_masks)==0 and np.max(train_masks)==1)
 
-    print "\ntrain images/masks shape:"
-    print train_imgs.shape
-    print "train images range (min-max): " +str(np.min(train_imgs)) +' - '+str(np.max(train_imgs))
-    print "train masks are within 0-1\n"
+    print ("\ntrain images/masks shape:")
+    print (train_imgs.shape)
+    print ("train images range (min-max): " +str(np.min(train_imgs)) +' - '+str(np.max(train_imgs)))
+    print ("train masks are within 0-1\n")
 
     #extract the TRAINING patches from the full images
     patches_imgs_train, patches_masks_train = extract_random(train_imgs,train_masks,patch_height,patch_width,N_subimgs,inside_FOV)
     data_consistency_check(patches_imgs_train, patches_masks_train)
 
-    print "\ntrain PATCHES images/masks shape:"
-    print patches_imgs_train.shape
-    print "train PATCHES images range (min-max): " +str(np.min(patches_imgs_train)) +' - '+str(np.max(patches_imgs_train))
+    print ("\ntrain PATCHES images/masks shape:")
+    print (patches_imgs_train.shape)
+    print ("train PATCHES images range (min-max): " +str(np.min(patches_imgs_train)) +' - '+str(np.max(patches_imgs_train)))
 
     return patches_imgs_train, patches_masks_train#, patches_imgs_test, patches_masks_test
 
@@ -70,19 +70,19 @@ def get_data_testing(DRIVE_test_imgs_original, DRIVE_test_groudTruth, Imgs_to_te
     #check masks are within 0-1
     assert(np.max(test_masks)==1  and np.min(test_masks)==0)
 
-    print "\ntest images/masks shape:"
-    print test_imgs.shape
-    print "test images range (min-max): " +str(np.min(test_imgs)) +' - '+str(np.max(test_imgs))
-    print "test masks are within 0-1\n"
+    print ("\ntest images/masks shape:")
+    print (test_imgs.shape)
+    print ("test images range (min-max): " +str(np.min(test_imgs)) +' - '+str(np.max(test_imgs)))
+    print ("test masks are within 0-1\n")
 
     #extract the TEST patches from the full images
     patches_imgs_test = extract_ordered(test_imgs,patch_height,patch_width)
     patches_masks_test = extract_ordered(test_masks,patch_height,patch_width)
     data_consistency_check(patches_imgs_test, patches_masks_test)
 
-    print "\ntest PATCHES images/masks shape:"
-    print patches_imgs_test.shape
-    print "test PATCHES images range (min-max): " +str(np.min(patches_imgs_test)) +' - '+str(np.max(patches_imgs_test))
+    print ("\ntest PATCHES images/masks shape:")
+    print (patches_imgs_test.shape)
+    print ("test PATCHES images range (min-max): " +str(np.min(patches_imgs_test)) +' - '+str(np.max(patches_imgs_test)))
 
     return patches_imgs_test, patches_masks_test
 
@@ -106,19 +106,19 @@ def get_data_testing_overlap(DRIVE_test_imgs_original, DRIVE_test_groudTruth, Im
     #check masks are within 0-1
     assert(np.max(test_masks)==1  and np.min(test_masks)==0)
 
-    print "\ntest images shape:"
-    print test_imgs.shape
-    print "\ntest mask shape:"
-    print test_masks.shape
-    print "test images range (min-max): " +str(np.min(test_imgs)) +' - '+str(np.max(test_imgs))
-    print "test masks are within 0-1\n"
+    print ("\ntest images shape:")
+    print (test_imgs.shape)
+    print ("\ntest mask shape:")
+    print (test_masks.shape)
+    print ("test images range (min-max): " +str(np.min(test_imgs)) +' - '+str(np.max(test_imgs)))
+    print ("test masks are within 0-1\n")
 
     #extract the TEST patches from the full images
     patches_imgs_test = extract_ordered_overlap(test_imgs,patch_height,patch_width,stride_height,stride_width)
 
-    print "\ntest PATCHES images shape:"
-    print patches_imgs_test.shape
-    print "test PATCHES images range (min-max): " +str(np.min(patches_imgs_test)) +' - '+str(np.max(patches_imgs_test))
+    print ("\ntest PATCHES images shape:")
+    print (patches_imgs_test.shape)
+    print ("test PATCHES images range (min-max): " +str(np.min(patches_imgs_test)) +' - '+str(np.max(patches_imgs_test)))
 
     return patches_imgs_test, test_imgs.shape[2], test_imgs.shape[3], test_masks
 
@@ -137,7 +137,7 @@ def data_consistency_check(imgs,masks):
 #  -- Inside OR in full image
 def extract_random(full_imgs,full_masks, patch_h,patch_w, N_patches, inside=True):
     if (N_patches%full_imgs.shape[0] != 0):
-        print "N_patches: plase enter a multiple of 20"
+        print ("N_patches: plase enter a multiple of 20")
         exit()
     assert (len(full_imgs.shape)==4 and len(full_masks.shape)==4)  #4D arrays
     assert (full_imgs.shape[1]==1 or full_imgs.shape[1]==3)  #check the channel is 1 or 3
@@ -149,7 +149,7 @@ def extract_random(full_imgs,full_masks, patch_h,patch_w, N_patches, inside=True
     img_w = full_imgs.shape[3] #width of the full image
     # (0,0) in the center of the image
     patch_per_img = int(N_patches/full_imgs.shape[0])  #N_patches equally divided in the full images
-    print "patches per full image: " +str(patch_per_img)
+    print ("patches per full image: " +str(patch_per_img))
     iter_tot = 0   #iter over the total numbe rof patches (N_patches)
     for i in range(full_imgs.shape[0]):  #loop over the full images
         k=0
@@ -191,11 +191,11 @@ def extract_ordered(full_imgs, patch_h, patch_w):
     img_w = full_imgs.shape[3] #width of the full image
     N_patches_h = int(img_h/patch_h) #round to lowest int
     if (img_h%patch_h != 0):
-        print "warning: " +str(N_patches_h) +" patches in height, with about " +str(img_h%patch_h) +" pixels left over"
+        print ("warning: " +str(N_patches_h) +" patches in height, with about " +str(img_h%patch_h) +" pixels left over")
     N_patches_w = int(img_w/patch_w) #round to lowest int
     if (img_h%patch_h != 0):
-        print "warning: " +str(N_patches_w) +" patches in width, with about " +str(img_w%patch_w) +" pixels left over"
-    print "number of patches per image: " +str(N_patches_h*N_patches_w)
+        print ("warning: " +str(N_patches_w) +" patches in width, with about " +str(img_w%patch_w) +" pixels left over")
+    print ("number of patches per image: " +str(N_patches_h*N_patches_w))
     N_patches_tot = (N_patches_h*N_patches_w)*full_imgs.shape[0]
     patches = np.empty((N_patches_tot,full_imgs.shape[1],patch_h,patch_w))
 
@@ -218,22 +218,22 @@ def paint_border_overlap(full_imgs, patch_h, patch_w, stride_h, stride_w):
     leftover_h = (img_h-patch_h)%stride_h  #leftover on the h dim
     leftover_w = (img_w-patch_w)%stride_w  #leftover on the w dim
     if (leftover_h != 0):  #change dimension of img_h
-        print "\nthe side H is not compatible with the selected stride of " +str(stride_h)
-        print "img_h " +str(img_h) + ", patch_h " +str(patch_h) + ", stride_h " +str(stride_h)
-        print "(img_h - patch_h) MOD stride_h: " +str(leftover_h)
-        print "So the H dim will be padded with additional " +str(stride_h - leftover_h) + " pixels"
+        print ("\nthe side H is not compatible with the selected stride of " +str(stride_h))
+        print ("img_h " +str(img_h) + ", patch_h " +str(patch_h) + ", stride_h " +str(stride_h))
+        print ("(img_h - patch_h) MOD stride_h: " +str(leftover_h))
+        print ("So the H dim will be padded with additional " +str(stride_h - leftover_h) + " pixels")
         tmp_full_imgs = np.zeros((full_imgs.shape[0],full_imgs.shape[1],img_h+(stride_h-leftover_h),img_w))
         tmp_full_imgs[0:full_imgs.shape[0],0:full_imgs.shape[1],0:img_h,0:img_w] = full_imgs
         full_imgs = tmp_full_imgs
     if (leftover_w != 0):   #change dimension of img_w
-        print "the side W is not compatible with the selected stride of " +str(stride_w)
-        print "img_w " +str(img_w) + ", patch_w " +str(patch_w) + ", stride_w " +str(stride_w)
-        print "(img_w - patch_w) MOD stride_w: " +str(leftover_w)
-        print "So the W dim will be padded with additional " +str(stride_w - leftover_w) + " pixels"
+        print ("the side W is not compatible with the selected stride of " +str(stride_w))
+        print ("img_w " +str(img_w) + ", patch_w " +str(patch_w) + ", stride_w " +str(stride_w))
+        print ("(img_w - patch_w) MOD stride_w: " +str(leftover_w))
+        print ("So the W dim will be padded with additional " +str(stride_w - leftover_w) + " pixels")
         tmp_full_imgs = np.zeros((full_imgs.shape[0],full_imgs.shape[1],full_imgs.shape[2],img_w+(stride_w - leftover_w)))
         tmp_full_imgs[0:full_imgs.shape[0],0:full_imgs.shape[1],0:full_imgs.shape[2],0:img_w] = full_imgs
         full_imgs = tmp_full_imgs
-    print "new full images shape: \n" +str(full_imgs.shape)
+    print ("new full images shape: \n" +str(full_imgs.shape))
     return full_imgs
 
 #Divide all the full_imgs in pacthes
@@ -245,9 +245,9 @@ def extract_ordered_overlap(full_imgs, patch_h, patch_w,stride_h,stride_w):
     assert ((img_h-patch_h)%stride_h==0 and (img_w-patch_w)%stride_w==0)
     N_patches_img = ((img_h-patch_h)//stride_h+1)*((img_w-patch_w)//stride_w+1)  #// --> division between integers
     N_patches_tot = N_patches_img*full_imgs.shape[0]
-    print "Number of patches on h : " +str(((img_h-patch_h)//stride_h+1))
-    print "Number of patches on w : " +str(((img_w-patch_w)//stride_w+1))
-    print "number of patches per image: " +str(N_patches_img) +", totally for this dataset: " +str(N_patches_tot)
+    print ("Number of patches on h : " +str(((img_h-patch_h)//stride_h+1)))
+    print ("Number of patches on w : " +str(((img_w-patch_w)//stride_w+1)))
+    print ("number of patches per image: " +str(N_patches_img) +", totally for this dataset: " +str(N_patches_tot))
     patches = np.empty((N_patches_tot,full_imgs.shape[1],patch_h,patch_w))
     iter_tot = 0   #iter over the total number of patches (N_patches)
     for i in range(full_imgs.shape[0]):  #loop over the full images
@@ -268,12 +268,12 @@ def recompone_overlap(preds, img_h, img_w, stride_h, stride_w):
     N_patches_h = (img_h-patch_h)//stride_h+1
     N_patches_w = (img_w-patch_w)//stride_w+1
     N_patches_img = N_patches_h * N_patches_w
-    print "N_patches_h: " +str(N_patches_h)
-    print "N_patches_w: " +str(N_patches_w)
-    print "N_patches_img: " +str(N_patches_img)
+    print ("N_patches_h: " +str(N_patches_h))
+    print ("N_patches_w: " +str(N_patches_w))
+    print ("N_patches_img: " +str(N_patches_img))
     assert (preds.shape[0]%N_patches_img==0)
     N_full_imgs = preds.shape[0]//N_patches_img
-    print "According to the dimension inserted, there are " +str(N_full_imgs) +" full images (of " +str(img_h)+"x" +str(img_w) +" each)"
+    print ("According to the dimension inserted, there are " +str(N_full_imgs) +" full images (of " +str(img_h)+"x" +str(img_w) +" each)")
     full_prob = np.zeros((N_full_imgs,preds.shape[1],img_h,img_w))  #itialize to zero mega array with sum of Probabilities
     full_sum = np.zeros((N_full_imgs,preds.shape[1],img_h,img_w))
 
@@ -287,7 +287,7 @@ def recompone_overlap(preds, img_h, img_w, stride_h, stride_w):
     assert(k==preds.shape[0])
     assert(np.min(full_sum)>=1.0)  #at least one
     final_avg = full_prob/full_sum
-    print final_avg.shape
+    print (final_avg.shape)
     assert(np.max(final_avg)<=1.0) #max value for a pixel is 1.0
     assert(np.min(final_avg)>=0.0) #min value for a pixel is 0.0
     return final_avg

diff --git a/lib/help_functions.py b/lib/help_functions.py
@@ -85,7 +85,7 @@ def pred_to_imgs(pred, patch_height, patch_width, mode="original"):
                 else:
                     pred_images[i,pix]=0
     else:
-        print "mode " +str(mode) +" not recognized, it can be 'original' or 'threshold'"
+        print ("mode " +str(mode) +" not recognized, it can be 'original' or 'threshold'")
         exit()
     pred_images = np.reshape(pred_images,(pred_images.shape[0],1, patch_height, patch_width))
     return pred_images
diff --git a/prepare_datasets_DRIVE.py b/prepare_datasets_DRIVE.py
@@ -40,12 +40,12 @@ def get_datasets(imgs_dir,groundTruth_dir,borderMasks_dir,train_test="null"):
     for path, subdirs, files in os.walk(imgs_dir): #list all files, directories in the path
         for i in range(len(files)):
             #original
-            print "original image: " +files[i]
+            print ("original image: " +files[i])
             img = Image.open(imgs_dir+files[i])
             imgs[i] = np.asarray(img)
             #corresponding ground truth
             groundTruth_name = files[i][0:2] + "_manual1.gif"
-            print "ground truth name: " + groundTruth_name
+            print ("ground truth name: " + groundTruth_name)
             g_truth = Image.open(groundTruth_dir + groundTruth_name)
             groundTruth[i] = np.asarray(g_truth)
             #corresponding border masks
@@ -55,17 +55,17 @@ def get_datasets(imgs_dir,groundTruth_dir,borderMasks_dir,train_test="null"):
             elif train_test=="test":
                 border_masks_name = files[i][0:2] + "_test_mask.gif"
             else:
-                print "specify if train or test!!"
+                print ("specify if train or test!!")
                 exit()
-            print "border masks name: " + border_masks_name
+            print ("border masks name: " + border_masks_name)
             b_mask = Image.open(borderMasks_dir + border_masks_name)
             border_masks[i] = np.asarray(b_mask)
 
-    print "imgs max: " +str(np.max(imgs))
-    print "imgs min: " +str(np.min(imgs))
+    print ("imgs max: " +str(np.max(imgs)))
+    print ("imgs min: " +str(np.min(imgs)))
     assert(np.max(groundTruth)==255 and np.max(border_masks)==255)
     assert(np.min(groundTruth)==0 and np.min(border_masks)==0)
-    print "ground truth and border masks are correctly withih pixel value range 0-255 (black-white)"
+    print ("ground truth and border masks are correctly withih pixel value range 0-255 (black-white)")
     #reshaping for my standard tensors
     imgs = np.transpose(imgs,(0,3,1,2))
     assert(imgs.shape == (Nimgs,channels,height,width))
@@ -79,14 +79,14 @@ def get_datasets(imgs_dir,groundTruth_dir,borderMasks_dir,train_test="null"):
     os.makedirs(dataset_path)
 #getting the training datasets
 imgs_train, groundTruth_train, border_masks_train = get_datasets(original_imgs_train,groundTruth_imgs_train,borderMasks_imgs_train,"train")
-print "saving train datasets"
+print ("saving train datasets")
 write_hdf5(imgs_train, dataset_path + "DRIVE_dataset_imgs_train.hdf5")
 write_hdf5(groundTruth_train, dataset_path + "DRIVE_dataset_groundTruth_train.hdf5")
 write_hdf5(border_masks_train,dataset_path + "DRIVE_dataset_borderMasks_train.hdf5")
 
 #getting the testing datasets
 imgs_test, groundTruth_test, border_masks_test = get_datasets(original_imgs_test,groundTruth_imgs_test,borderMasks_imgs_test,"test")
-print "saving test datasets"
+print ("saving test datasets")
 write_hdf5(imgs_test,dataset_path + "DRIVE_dataset_imgs_test.hdf5")
 write_hdf5(groundTruth_test, dataset_path + "DRIVE_dataset_groundTruth_test.hdf5")
 write_hdf5(border_masks_test,dataset_path + "DRIVE_dataset_borderMasks_test.hdf5")
diff --git a/run_testing.py b/run_testing.py
@@ -5,11 +5,11 @@
 ##################################################
 
 import os, sys
-import ConfigParser
+import configparser
 
 
 #config file to read from
-config = ConfigParser.RawConfigParser()
+config = configparser.RawConfigParser()
 config.readfp(open(r'./configuration.txt'))
 #===========================================
 #name of the experiment!!
@@ -20,7 +20,7 @@
 
 #create a folder for the results if not existing already
 result_dir = name_experiment
-print "\n1. Create directory for the results (if not already existing)"
+print ("\n1. Create directory for the results (if not already existing)")
 if os.path.exists(result_dir):
     pass
 elif sys.platform=='win32':
@@ -31,8 +31,8 @@
 
 # finally run the prediction
 if nohup:
-    print "\n2. Run the prediction on GPU  with nohup"
+    print ("\n2. Run the prediction on GPU  with nohup")
     os.system(run_GPU +' nohup python -u ./src/retinaNN_predict.py > ' +'./'+name_experiment+'/'+name_experiment+'_prediction.nohup')
 else:
-    print "\n2. Run the prediction on GPU (no nohup)"
+    print ("\n2. Run the prediction on GPU (no nohup)")
     os.system(run_GPU +' python ./src/retinaNN_predict.py')
diff --git a/run_training.py b/run_training.py
@@ -5,12 +5,12 @@
 ##################################################
 
 import os, sys
-import ConfigParser
+import configparser
 
 
 #config file to read from
-config = ConfigParser.RawConfigParser()
-config.readfp(open(r'./configuration.txt'))
+config = configparser.RawConfigParser()
+config.read_file(open(r'./configuration.txt'))
 #===========================================
 #name of the experiment
 name_experiment = config.get('experiment name', 'name')
@@ -20,26 +20,26 @@
 
 #create a folder for the results
 result_dir = name_experiment
-print "\n1. Create directory for the results (if not already existing)"
+print ("\n1. Create directory for the results (if not already existing)")
 if os.path.exists(result_dir):
-    print "Dir already existing"
+    print ("Dir already existing")
 elif sys.platform=='win32':
     os.system('mkdir ' + result_dir)
 else:
     os.system('mkdir -p ' +result_dir)
 
-print "copy the configuration file in the results folder"
+print ("copy the configuration file in the results folder")
 if sys.platform=='win32':
     os.system('copy configuration.txt .\\' +name_experiment+'\\'+name_experiment+'_configuration.txt')
 else:
     os.system('cp configuration.txt ./' +name_experiment+'/'+name_experiment+'_configuration.txt')
 
 # run the experiment
 if nohup:
-    print "\n2. Run the training on GPU with nohup"
-    os.system(run_GPU +' nohup python -u ./src/retinaNN_training.py > ' +'./'+name_experiment+'/'+name_experiment+'_training.nohup')
+    print ("\n2. Run the training on GPU with nohup")
+    os.system(run_GPU +' start /min python3 -u ./src/retinaNN_training.py > ' +'./'+name_experiment+'/'+name_experiment+'_training.nohup')
 else:
-    print "\n2. Run the training on GPU (no nohup)"
-    os.system(run_GPU +' python ./src/retinaNN_training.py')
+    print ("\n2. Run the training on GPU (no nohup)")
+    os.system(run_GPU +' python3 ./src/retinaNN_training.py')
 
 #Prediction/testing is run with a different script