--- a
+++ b/augmentation.py
@@ -0,0 +1,64 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Jun  3 10:46:04 2019
+
+@author: Josefine
+"""
+
+import re
+import glob
+import sitk_functions as func
+import SimpleITK as sitk
+
+def natural_sort(l): 
+    convert = lambda text: int(text) if text.isdigit() else text.lower() 
+    alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', key) ] 
+    return sorted(l, key = alphanum_key)
+
+filename_img = natural_sort(glob.glob('WHS/ct_train_test/ct_train/*_image.nii.gz')) # list of file names
+filename_label = natural_sort(glob.glob('WHS/ct_train_test/ct_train/*_label.nii.gz')) # list of file names
+
+for k in range(len(filename_img)):
+    print('Load image',(k+1))
+    img_sitk = sitk.ReadImage(filename_img[k])
+    label_sitk = sitk.ReadImage(filename_label[k])
+    filter = sitk.MinimumMaximumImageFilter()
+    filter.Execute(img_sitk)
+    min_val = filter.GetMinimum()
+    
+    # NORMAL
+    sitk.WriteImage(img_sitk,'WHS/Augment_data/normal_{}_image.nii'.format(k))
+    sitk.WriteImage(label_sitk,'WHS/Augment_data/normal_{}_label.nii'.format(k))
+
+#    # ROTATION
+#    [img_rot, label_rot] = func.affine_rotate(img_sitk,label_sitk,min_val)
+#    sitk.WriteImage(img_rot,'WHS/Augment_data/rot_{}_image.nii'.format(k))
+#    sitk.WriteImage(label_rot,'WHS/Augment_data/rot_{}_label.nii'.format(k))
+
+#    # SHEAR
+#    [img_sh, label_sh] = func.affine_shear(img_sitk,label_sitk,min_val)
+#    sitk.WriteImage(img_sh,'WHS/Augment_data/sh_{}_image.nii'.format(k))
+#    sitk.WriteImage(label_sh,'WHS/Augment_data/sh_{}_label.nii'.format(k))
+#    
+#    # Intensity
+#    l1 = func.mult_and_add_intensity_fields(img_sitk)
+#    sitk.WriteImage(l1,'WHS/Augment_data/intensity_{}_image.nii'.format(k))
+#    sitk.WriteImage(label_sitk,'WHS/Augment_data/intensity_{}_label.nii'.format(k))
+
+#    # B SPLINE
+    numcontrolpoints = 5
+    stdDeform = 15
+    dim = 3
+    [img_bspline, label_bspline] = func.BSplineDeform(img_sitk,label_sitk, dim, numcontrolpoints, stdDeform,min_val)
+    sitk.WriteImage(img_bspline,'WHS/Augment_data/bspline_{}_image.nii'.format(k))
+    sitk.WriteImage(label_bspline,'WHS/Augment_data/bspline_{}_label.nii'.format(k))
+
+    # B SPLINE
+    numcontrolpoints = 10
+    stdDeform = 10
+    dim = 3
+    [img_bspline, label_bspline] = func.BSplineDeform(img_sitk,label_sitk, dim, numcontrolpoints, stdDeform,min_val)
+    sitk.WriteImage(img_bspline,'WHS/Augment_data/bspline2_{}_image.nii'.format(k))
+    sitk.WriteImage(label_bspline,'WHS/Augment_data/bspline2_{}_label.nii'.format(k))
+    print('Finished with image',(k+1))