--- a
+++ b/Classification/crop_roi_axial.py
@@ -0,0 +1,138 @@
+import os
+import xml.etree.ElementTree as ET
+import cv2
+
+cwd = './Axial_1-491_10751x2jpgXmls_ResnetRecrop_Jun152020'
+center_dir = 'center-crop'
+left_dir = 'left-crop'
+right_dir = 'right-crop'
+
+out_dirs = [center_dir, left_dir, right_dir]
+grading = ['1', '2', '3', '4']
+
+center_label_file = 'Axial_1-491_10751x2_Jun142020-axial-center-label.txt'
+right_label_file = 'Axial_1-491_10751x2_Jun142020-axial-right-label.txt'
+left_label_file = 'Axial_1-491_10751x2_Jun142020-axial-left-label.txt'
+
+# 150% scale, use scale_factor = 0.5
+scale_factor = 0.5
+
+for e in out_dirs:
+    if not os.path.exists(e):
+        os.makedirs(e)
+
+    for ee in grading:
+        if not os.path.exists(os.path.join(e, ee)):
+            os.makedirs(os.path.join(e, ee))
+
+center_label = {}
+right_label = {}
+left_label = {}
+
+with open(center_label_file, 'r') as f:
+    lines = f.readlines()
+    for e in lines:
+        tmp = e.strip().split(' ')
+        center_label[tmp[0]] = tmp[1]
+
+with open(right_label_file, 'r') as f:
+    lines = f.readlines()
+    for e in lines:
+        tmp = e.strip().split(' ')
+        right_label[tmp[0]] = tmp[1]
+
+with open(left_label_file, 'r') as f:
+    lines = f.readlines()
+    for e in lines:
+        tmp = e.strip().split(' ')
+        left_label[tmp[0]] = tmp[1]
+
+# print(center_label)
+# print(right_label)
+# print(left_label)
+
+# exit(0)
+
+
+def scale_crop(xmin, xmax, ymin, ymax, factor, img_shape):
+    """
+    the imgs top left corner is (0,0),
+    x min-max is from point A,
+    y min-max is from point B
+    """
+    cropped_w = xmax - xmin
+    cropped_h = ymax - ymin
+    xmin -= ((cropped_w * factor) // 2)
+    ymin -= ((cropped_h * factor) // 2)
+
+    xmax += ((cropped_w * factor) // 2)
+    ymax += ((cropped_h * factor) // 2)
+
+    # cv2 img shape information
+    height = img_shape[0]
+    width = img_shape[1]
+
+    return (
+            int(max(xmin, 0)),
+            int(min(xmax, width)),
+            int(max(ymin, 0)),
+            int(min(ymax, height))
+            )
+
+
+for file in os.listdir(cwd):
+    if '.xml' in file:
+        print(file)
+        img = cv2.imread(os.path.join(cwd, file.replace('xml', 'JPG')), 0)
+        print(img.shape)
+
+        # print(np.array_equal(img[:,:,0], img[:,:,1]))
+        # print(np.array_equal(img[:,:,0], img[:,:,2]))
+        # print(np.array_equal(img[:,:,1], img[:,:,2]))
+
+        # for k in range(0, 3):
+        #   for i in range(0, 10):
+        #       tmp = ''
+        #       for j in range(0, 10):
+        #           tmp += str(img[i,j,k]) + ' '
+        #       print(tmp + '\n')
+
+        #   print('\n\n')
+
+        data = ET.parse(os.path.join(cwd, file))
+        root = data.getroot()
+        for o in root.findall('object'):
+            name = o.find('name').text
+            xmin = int(o.find('bndbox').find('xmin').text)
+            xmax = int(o.find('bndbox').find('xmax').text)
+            ymin = int(o.find('bndbox').find('ymin').text)
+            ymax = int(o.find('bndbox').find('ymax').text)
+
+            print(">>>>before scaling, xmin, xmax, ymin, ymax: ", xmin, xmax, ymin, ymax)
+
+            (xmin, xmax, ymin, ymax) = scale_crop(xmin, xmax, ymin, ymax, scale_factor, img.shape)
+
+            print("<<<<after scaling, xmin, xmax, ymin, ymax: ", xmin, xmax, ymin, ymax)
+
+            cropped_img = img[ymin:ymax, xmin:xmax]
+
+            # cv2.imshow('image', cropped_img)
+            # cv2.waitKey(0)
+            # exit(0)
+
+            # print(file)
+            # exit(0)
+
+            if name == 'center':
+                tmp = center_label[file]
+                if not cv2.imwrite(os.path.join(center_dir, tmp, file.replace('xml', 'png')), cropped_img):
+                    print(os.path.join(center_dir, tmp, file.replace('xml', 'jpg')))
+                    raise Exception("Could not write image")
+            elif name == 'right':
+                tmp = right_label[file]
+                if not cv2.imwrite(os.path.join(right_dir, tmp, file.replace('xml', 'png')), cropped_img):
+                    raise Exception("Could not write image")
+            else:
+                tmp = left_label[file]
+                if not cv2.imwrite(os.path.join(left_dir, tmp, file.replace('xml', 'png')), cropped_img):
+                    raise Exception("Could not write image")